VFB scRNAseq Ontology for dataset FBlc0005362
type: Ontology
description: An ontology of Drosophila melanogaster scRNAseq data from a single dataset (FBlc0005362). This information is taken from FlyBase, which sources it from the EMBL-EBI Single Cell Expression Atlas, which compiles scRNAseq data from multiple sources.

definition
type: AnnotationProperty
IAO_0000111: definition
IAO_0000114: IAO_0000122
definition: A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
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.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition.
IAO_0000116: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
has exact synonym: DEFINITION
label: textual definition

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

database_cross_reference
type: AnnotationProperty
definition: Reference database or publication source.

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: 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.
IAO_0000116: 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
RO_0001900: RO_0001901
RO_0040042: BFO_0000002
RO_0040042: BFO_0000003
RO_0040042: BFO_0000004
RO_0040042: BFO_0000017
RO_0040042: BFO_0000019
RO_0040042: BFO_0000020
RO_0040042: BFO_0000031
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
IAO_0000116: 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.
IAO_0000116: 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
RO_0001900: RO_0001901
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

realized in
type: ObjectProperty
inverse of: realizes
domain: BFO_0000017
range: BFO_0000015
IAO_0000111: realized in
IAO_0000112: this disease is realized in this disease course
IAO_0000112: this fragility is realized in this shattering
IAO_0000112: this investigator role is realized in this investigation
IAO_0000118: is realized by
IAO_0000118: realized_in
IAO_0000600: [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])
comment: 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

realizes
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000017
IAO_0000111: realizes
IAO_0000112: this disease course realizes this disease
IAO_0000112: this investigation realizes this investigator role
IAO_0000112: this shattering realizes this fragility
IAO_0000600: 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])
comment: 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

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: BFO_0000003
range: BFO_0000003
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
IAO_0000111: preceded by
definition: 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.
IAO_0000116: 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.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: BFO_0000003
range: BFO_0000003
property chain axiom: part of
property chain axiom: happens during
IAO_0000111: precedes
definition: 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.
in subset: ro-eco

substage of
type: ObjectProperty
sub property of: occurrent part of
sub property of: happens during
type: TransitiveProperty
definition: A relation between a developmental stage and another, larger developmental stage during which it happens.
has OBO namespace: relationship
id: FBdv:00018001
comment: Creating this relation as a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO.

Axiom
annotated source: substage of
annotated property: definition
annotated target: A relation between a developmental stage and another, larger developmental stage during which it happens.
database_cross_reference: FBC:DPG

has_specified_input
type: ObjectProperty
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
IAO_0000111: has_specified_input
IAO_0000112: see is_input_of example_of_usage
IAO_0000114: IAO_0000122
definition: The inverse property of is_specified_input_of
IAO_0000116: 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.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Larry Hunter
IAO_0000117: PERSON: Melanie Coutot

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
IAO_0000111: is_specified_input_of
IAO_0000112: 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
IAO_0000114: IAO_0000122
definition: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000117: PERSON:Bjoern Peters

has_specified_output
type: ObjectProperty
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
IAO_0000111: has_specified_output
IAO_0000114: IAO_0000122
definition: The inverse property of is_specified_output_of
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Larry Hunter
IAO_0000117: PERSON: Melanie Courtot

is_specified_output_of
type: ObjectProperty
sub property of: participates in
range: planned process
IAO_0000111: is_specified_output_of
IAO_0000114: IAO_0000122
definition: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000117: PERSON:Bjoern Peters

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: IAO_0000005
IAO_0000111: achieves_planned_objective
IAO_0000112: A cell sorting process achieves the objective specification 'material separation objective'
IAO_0000114: IAO_0000120
definition: 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.
IAO_0000117: BP, AR, PPPB branch
IAO_0000119: PPPB branch derived
IAO_0000232: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch

objective_achieved_by
type: ObjectProperty
domain: IAO_0000005
range: planned process
IAO_0000111: objective_achieved_by
IAO_0000114: IAO_0000122
definition: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
IAO_0000117: OBI
IAO_0000119: OBI

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000111: inheres in
IAO_0000112: this fragility is a characteristic of this vase
IAO_0000112: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
IAO_0000118: inheres_in
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: BFO_0000020
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
definition: Inverse of characteristic_of
IAO_0000116: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
RO_0001900: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: BFO_0000002
range: BFO_0000003
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in

has participant
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000002
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: 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.
IAO_0000118: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: BFO_0000031
range: BFO_0000020
IAO_0000112: 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 journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: 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).
definition: A relationship between a generically dependent continuant and a specifically 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. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: BFO_0000020
range: BFO_0000031
IAO_0000112: 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).
IAO_0000112: 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).
definition: 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.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
IAO_0000116: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
IAO_0000118: is role of
IAO_0000118: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has role
type: ObjectProperty
sub property of: has characteristic
domain: BFO_0000004
range: BFO_0000023
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
IAO_0000116: 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.
IAO_0000118: has_role

has synaptic terminal of
type: ObjectProperty
sub property of: overlaps
inverse of: has synaptic terminal in
IAO_0000117: https://orcid.org/0000-0002-7073-9172
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

occurrent part of
type: ObjectProperty
sub property of: part of
sub property of: causally upstream of or within
domain: BFO_0000003
range: BFO_0000003
definition: A part of relation that applies only between occurrents.

during which ends
type: ObjectProperty
sub property of: temporally related to
inverse of: ends during
IAO_0000117: David Osumi-Sutherland
in subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

encompasses
type: ObjectProperty
sub property of: during which starts
inverse of: happens during
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: di
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
IAO_0000117: David Osumi-Sutherland
in subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
IAO_0000117: David Osumi-Sutherland
IAO_0000118: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

during which starts
type: ObjectProperty
sub property of: temporally related to
inverse of: starts during
IAO_0000117: David Osumi-Sutherland
in subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

immediately precedes
type: ObjectProperty
sub property of: precedes
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: David Osumi-Sutherland
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
in subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: BFO_0000003
range: BFO_0000003
IAO_0000117: David Osumi-Sutherland
IAO_0000118: io
in subset: ro-eco
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: starts during
sub property of: ends during
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
IAO_0000118: d
IAO_0000118: during
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
IAO_0000117: David Osumi-Sutherland
IAO_0000118: o
IAO_0000118: overlaps
in subset: ro-eco
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

has soma location
type: ObjectProperty
sub property of: overlaps
domain: CL_0000540
range: UBERON_0000465
property chain axiom: part of
IAO_0000114: IAO_0000125
definition: Relation between a neuron and a material anatomical entity that its soma is part of.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
RO_0001900: RO_0001901

has postsynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
inverse of: has presynaptic terminal in
domain: CL_0000540
property chain axiom: part of
IAO_0000114: IAO_0000125
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: synapsed in
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has presynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
domain: CL_0000540
property chain axiom: part of
IAO_0000114: IAO_0000125
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000118: synapses in
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has synaptic terminal in
type: ObjectProperty
sub property of: overlaps
domain: CL_0000540
property chain axiom: part of
IAO_0000114: IAO_0000125
definition: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: has synapse in
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000114: IAO_0000125
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

continuous with
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
domain: BFO_0000004
range: BFO_0000004
IAO_0000114: IAO_0000125
definition: X continuous_with Y if and only if X and Y share a fiat boundary.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: connected to
IAO_0000232: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
RO_0001900: RO_0001901

develops from
type: ObjectProperty
sub property of: has developmental contribution from
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: BFO_0000004
range: BFO_0000004
IAO_0000114: IAO_0000125
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
IAO_0000117: https://orcid.org/0000-0001-9114-8737
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
IAO_0000114: IAO_0000125
definition: inverse of develops from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
in subset: RO_0002259

expressed in
type: ObjectProperty
sub property of: genomically related to
inverse of: expresses
domain: BFO_0000002
domain: Class
  union of: BFO_0000031
  union of: BFO_0000040
range: UBERON_0000465
property chain axiom: part of
IAO_0000112: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
IAO_0000114: IAO_0000125
definition: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
IAO_0000117: https://orcid.org/0000-0002-6601-2165

capable of
type: ObjectProperty
sub property of: capable of part of
domain: BFO_0000004
range: BFO_0000015
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
in subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function in

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

temporally related to
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000003
IAO_0000114: IAO_0000125
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Allen's interval algebra
IAO_0000232: 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.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
in subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: BFO_0000015
IAO_0000114: IAO_0000125
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: consumes
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
property chain axiom: develops from
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: IAO_0000125
definition: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
IAO_0000114: IAO_0000125
definition: inverse of has developmental contribution from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: BFO_0000002
range: BFO_0000002
IAO_0000114: IAO_0000125
definition: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
IAO_0000116: false
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000125
definition: Inverse of developmentally preceded by
IAO_0000117: https://orcid.org/0000-0002-6601-2165

expresses
type: ObjectProperty
sub property of: genomically related to
IAO_0000114: IAO_0000125
definition: y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

genomically related to
type: ObjectProperty
domain: BFO_0000002
range: BFO_0000002
definition: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
IAO_0000112: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
IAO_0000118: is member of
IAO_0000118: member part of
IAO_0000119: SIO
RO_0001900: RO_0001901

has member
type: ObjectProperty
sub property of: has part
definition: has member is a mereological relation between a collection and an item.
IAO_0000119: SIO
RO_0001900: RO_0001901

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259
in subset: ro-eco

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
IAO_0000114: IAO_0000428
definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
IAO_0000114: IAO_0000428
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
IAO_0000116: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie[cell cut: 2047 characters, first 2000 kept]
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

Axiom
annotated source: causally related to
annotated property: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
database_cross_reference: https://en.wikipedia.org/wiki/Causality

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: influences (processual)
has related synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
in subset: RO_0002259

composed primarily of
type: ObjectProperty
sub property of: has part
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
definition: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
RO_0001900: RO_0001901
in subset: ro-eco

relation between physical entity and a process or stage
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000003
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.

existence overlaps
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
definition: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000003
range: BFO_0000003
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000040
range: BFO_0000015
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
IAO_0000119: causal-relations

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: BFO_0000031
range: BFO_0000004
property chain axiom: characteristic of
property chain axiom: is concretized as
IAO_0000112: Genetic information generically depend on molecules of DNA.
IAO_0000112: The novel *War and Peace* generically depends on this copy of the novel.
IAO_0000112: The pattern shared by chess boards generically depends on any chess board.
IAO_0000112: The score of a symphony g-depends on a copy of the score.
IAO_0000112: This pdf file generically depends on this server.
definition: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
IAO_0000119: [072-ISO]
has exact synonym: g-depends on

is carrier of
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000031
property chain axiom: concretizes
property chain axiom: has characteristic
IAO_0000112: Molecules of DNA are carriers of genetic information.
IAO_0000112: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
IAO_0000112: This hard drive is carrier of these data items.
definition: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
IAO_0000119: [072-ISO]

has synaptic IO in region
type: ObjectProperty
sub property of: has synaptic terminal in
property chain axiom: part of
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:26:52Z
has exact synonym: has synaptic input or output in

receives synaptic input in region
type: ObjectProperty
sub property of: has postsynaptic terminal in
sub property of: has synaptic IO in region
property chain axiom: part of
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:42:23Z

sends synaptic output to region
type: ObjectProperty
sub property of: has presynaptic terminal in
sub property of: has synaptic IO in region
property chain axiom: part of
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
created by: https://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:45:06Z

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
IAO_0000112: A diagnostic testing device utilizes a specimen.
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
IAO_0000232: A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
IAO_0000232: See github ticket https://github.com/oborel/obo-relations/issues/497
contributor: https://orcid.org/0000-0001-9625-1899
contributor: https://orcid.org/0000-0003-2620-0345
creation date: 2021-11-08T12:00:00Z
has broad synonym: utilizes

has assay method
type: ObjectProperty
sub property of: topObjectProperty
inverse of: is assay method of

is assay method of
type: ObjectProperty
sub property of: topObjectProperty

germ layer derivative
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: develops from
    some values from: germ layer
subclass of: BFO_0000002
subclass of: anatomical entity
subclass of: Restriction
  on property: develops from
  some values from: germ layer
definition: Any anatomical entity (FBbt:10000000) that develops from some germ layer (FBbt:00000110).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000000
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: germ layer derivative
annotated property: definition
annotated target: Any anatomical entity (FBbt:10000000) that develops from some germ layer (FBbt:00000110).
database_cross_reference: FlyBase:FBrf0043441
database_cross_reference: FlyBase:FBrf0053832

organism
type: Class
subclass of: multicellular structure
definition: An individual member of the species Drosophila melanogaster.
database_cross_reference: CARO:0000012
database_cross_reference: NCBITaxon:7227
database_cross_reference: UBERON:0000468
has OBO namespace: fly_anatomy.ontology
has related synonym: Drosophila
has related synonym: whole organism
id: FBbt:00000001
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: organism
annotated property: definition
annotated target: An individual member of the species Drosophila melanogaster.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

tagma
type: Class
subclass of: anterior-posterior subdivision of organism
subclass of: Restriction
  on property: part of
  some values from: organism
definition: One of the three main divisions of the whole organism formed from groups of segments.
database_cross_reference: UBERON:6000002
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000002
in subset: FB gloss
in subset: cur
in subset: larval OF

Axiom
annotated source: tagma
annotated property: definition
annotated target: One of the three main divisions of the whole organism formed from groups of segments.
database_cross_reference: FBC:GG

segment
type: Class
subclass of: anterior-posterior subdivision of organism
definition: One of the repeated divisions of the whole organism.
database_cross_reference: UBERON:0000914
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000003
in subset: FB gloss
in subset: cur
in subset: larval OF

Axiom
annotated source: segment
annotated property: definition
annotated target: One of the repeated divisions of the whole organism.
database_cross_reference: FBC:GG

head
type: Class
subclass of: tagma
definition: Anterior part of the organism, including mouthparts, some sensory structures and the brain.
database_cross_reference: UBERON:6000004
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000004
in subset: cur
in subset: larval OF

Axiom
annotated source: head
annotated property: definition
annotated target: Anterior part of the organism, including mouthparts, some sensory structures and the brain.
database_cross_reference: https://orcid.org/0000-0002-1373-1705

ocular segment
type: Class
subclass of: procephalic segment
definition: Head segment derived from the second embryonic segment (between the labral and antennal segments). In the larva, this segment includes Bolwig's organ.
database_cross_reference: UBERON:6000005
has OBO namespace: fly_anatomy.ontology
has related synonym: acron
id: FBbt:00000005
in subset: cur
comment: While classically this structure is not considered to be a segment, but rather to be the non-segmental acron - anterior to the first segment, this ontology follows Schmidt-Ott and colleagues (Schmidt-Ott et al., 1994, and Schmidt-Ott and Technau, 1992) in considering it to be the second segment (posterior to the labral segment in the segmenting embryo). This is based on relating gene expression in the early segmenting embryo to the effects of loss of function mutations of these genes on formation of larval head structures.

Axiom
annotated source: ocular segment
annotated property: definition
annotated target: Head segment derived from the second embryonic segment (between the labral and antennal segments). In the larva, this segment includes Bolwig's organ.
database_cross_reference: FlyBase:FBrf0055841
database_cross_reference: FlyBase:FBrf0075072

head segment
type: Class
equivalent class: Class
  intersection of: segment
  intersection of: Restriction
    on property: part of
    some values from: head
subclass of: segment
subclass of: Restriction
  on property: part of
  some values from: head
definition: Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).
database_cross_reference: UBERON:6000006
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000006
in subset: cur
in subset: larval OF

Axiom
annotated source: head segment
annotated property: definition
annotated target: Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).
database_cross_reference: FlyBase:FBrf0075072

procephalic segment
type: Class
subclass of: head segment
definition: A segment that is anterior to the gnathal segments.
database_cross_reference: UBERON:6000007
has exact synonym: pregnathal segment
has exact synonym: preoral segment
has OBO namespace: fly_anatomy.ontology
has related synonym: cephalic segment
has related synonym: procephalon
id: FBbt:00000007
in subset: FB gloss
in subset: cur
in subset: larval OF

Axiom
annotated source: procephalic segment
annotated property: definition
annotated target: A segment that is anterior to the gnathal segments.
database_cross_reference: FBC:GG

labral segment
type: Class
subclass of: procephalic segment
definition: Anteriormost procephalic segment, anterior to the ocular segment. In the adult it bears the clypeo-labrum.
database_cross_reference: UBERON:6000008
has OBO namespace: fly_anatomy.ontology
has related synonym: clypeo-labrum
id: FBbt:00000008
in subset: cur

Axiom
annotated source: labral segment
annotated property: definition
annotated target: Anteriormost procephalic segment, anterior to the ocular segment. In the adult it bears the clypeo-labrum.
database_cross_reference: FlyBase:FBrf0055841
database_cross_reference: FlyBase:FBrf0075072
database_cross_reference: FlyBase:FBrf0089570

antennal segment
type: Class
subclass of: procephalic segment
definition: Segment anterior to the intercalary segment. In the adult it bears the antennae.
database_cross_reference: UBERON:6000009
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000009
in subset: cur

Axiom
annotated source: antennal segment
annotated property: definition
annotated target: Segment anterior to the intercalary segment. In the adult it bears the antennae.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

embryo
type: Class
subclass of: organism
definition: An organism that is undergoing embryogenesis (Campos-Ortega and Hartenstein, 1997). Embryogenesis begins with a fertilized egg, and finishes with hatching at the end of embryonic stage 17 (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FBdv:00005289
database_cross_reference: UBERON:0000922
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000052
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryo
annotated property: definition
annotated target: An organism that is undergoing embryogenesis (Campos-Ortega and Hartenstein, 1997). Embryogenesis begins with a fertilized egg, and finishes with hatching at the end of embryonic stage 17 (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0039741
database_cross_reference: FlyBase:FBrf0089570

cleavage stage embryo
type: Class
subclass of: embryo
definition: Embryo that is in the cleavage stage, which encompasses the first 13 rapid divisions after fertilization, corresponding to embryonic stages 1-4, prior to cellularization (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997). The first seven divisions are synchronous (Campos-Ortega and Hartenstein, 1997). During the course of the subsequent three divisions, most of the nuclei approach the surface, to form the syncitial blastoderm (Campos-Ortega and Hartenstein, 1997). They then divide asynchronously a further three times, bringing the total number of cells to around 5000 (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FBdv:00000054
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000054

Axiom
annotated source: cleavage stage embryo
annotated property: definition
annotated target: Embryo that is in the cleavage stage, which encompasses the first 13 rapid divisions after fertilization, corresponding to embryonic stages 1-4, prior to cellularization (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997). The first seven divisions are synchronous (Campos-Ortega and Hartenstein, 1997). During the course of the subsequent three divisions, most of the nuclei approach the surface, to form the syncitial blastoderm (Campos-Ortega and Hartenstein, 1997). They then divide asynchronously a further three times, bringing the total number of cells to around 5000 (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0064803
database_cross_reference: FlyBase:FBrf0089570

germ layer
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: portion of tissue
subclass of: Restriction
  on property: develops into
  some values from: germ layer derivative
definition: Complex primordium that is formed during gastrulation (stage 6-7), when anlagen invaginate from the monolayer of the cellular blastoderm (Campos-Ortega and Hartenstein, 1997; Hartenstein, 2004). The invaginated anlagen become organized into the middle two layers of a three-layered tube structure (Campos-Ortega and Hartenstein, 1997). These three layers correspond to the three germ layers of the endoderm, mesoderm and ectoderm (from inner to outer, respectively), with each layer having distinct cell division patterns and cell fates (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: UBERON:0000923
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000110
in subset: EmbDevSlim
in subset: FB gloss
in subset: cur

Axiom
annotated source: germ layer
annotated property: definition
annotated target: Complex primordium that is formed during gastrulation (stage 6-7), when anlagen invaginate from the monolayer of the cellular blastoderm (Campos-Ortega and Hartenstein, 1997; Hartenstein, 2004). The invaginated anlagen become organized into the middle two layers of a three-layered tube structure (Campos-Ortega and Hartenstein, 1997). These three layers correspond to the three germ layers of the endoderm, mesoderm and ectoderm (from inner to outer, respectively), with each layer having distinct cell division patterns and cell fates (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0155831
database_cross_reference: FlyBase:FBrf0178740

ectoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: develops from
  some values from: ectoderm anlage
subclass of: Restriction
  on property: develops into
  some values from: ectodermal derivative
definition: Outermost germ layer of the embryo (Campos-Ortega and Hartenstein, 1997). It is formed from the ectoderm anlage, which includes the cells of the cellular blastoderm monolayer that do not invaginate during gastrulation (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: UBERON:0000924
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000111
in subset: EmbDevSlim
in subset: FB gloss
in subset: cur

Axiom
annotated source: ectoderm
annotated property: definition
annotated target: Outermost germ layer of the embryo (Campos-Ortega and Hartenstein, 1997). It is formed from the ectoderm anlage, which includes the cells of the cellular blastoderm monolayer that do not invaginate during gastrulation (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0155831
database_cross_reference: FlyBase:FBrf0244630

anterior ectoderm
type: Class
subclass of: BFO_0000002
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: develops from
  some values from: anterior ectoderm anlage
definition: The region of the ectoderm anterior to the cephalic furrow.
database_cross_reference: UBERON:6000119
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000119
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: anterior ectoderm
annotated property: definition
annotated target: The region of the ectoderm anterior to the cephalic furrow.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

embryonic tagma
type: Class
equivalent class: Class
  intersection of: tagma
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: tagma
subclass of: Restriction
  on property: part of
  some values from: embryo
definition: Any tagma of the embryo.
database_cross_reference: UBERON:6000137
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000137
in subset: cur

Axiom
annotated source: embryonic tagma
annotated property: definition
annotated target: Any tagma of the embryo.
database_cross_reference: FBC:Autogenerated

embryonic segment
type: Class
equivalent class: Class
  intersection of: segment
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: segment
subclass of: Restriction
  on property: part of
  some values from: embryo
definition: Any segment of the embryo.
database_cross_reference: UBERON:6000154
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000154
in subset: cur

Axiom
annotated source: embryonic segment
annotated property: definition
annotated target: Any segment of the embryo.
database_cross_reference: FBC:Autogenerated

embryonic head
type: Class
equivalent class: Class
  intersection of: head
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: head
subclass of: embryonic tagma
definition: Any head of the embryo.
database_cross_reference: UBERON:0008816
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000155
in subset: cur
in subset: larval OF

Axiom
annotated source: embryonic head
annotated property: definition
annotated target: Any head of the embryo.
database_cross_reference: FBC:Autogenerated

embryonic ocular segment
type: Class
equivalent class: Class
  intersection of: ocular segment
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: ocular segment
subclass of: embryonic procephalic segment
definition: Any ocular segment of the embryo.
has OBO namespace: fly_anatomy.ontology
has related synonym: embryonic acron
id: FBbt:00000156
in subset: cur

Axiom
annotated source: embryonic ocular segment
annotated property: definition
annotated target: Any ocular segment of the embryo.
database_cross_reference: FBC:Autogenerated

embryonic head segment
type: Class
equivalent class: Class
  intersection of: head segment
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: head segment
subclass of: embryonic segment
subclass of: Restriction
  on property: part of
  some values from: embryonic head
definition: Any head segment of the embryo.
database_cross_reference: UBERON:6000157
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000157
in subset: cur

Axiom
annotated source: embryonic head segment
annotated property: definition
annotated target: Any head segment of the embryo.
database_cross_reference: FlyBase:FBrf0075072

embryonic procephalic segment
type: Class
equivalent class: Class
  intersection of: procephalic segment
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: procephalic segment
subclass of: embryonic head segment
definition: Any procephalic segment of the embryo.
database_cross_reference: UBERON:6000158
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000158
in subset: cur

Axiom
annotated source: embryonic procephalic segment
annotated property: definition
annotated target: Any procephalic segment of the embryo.
database_cross_reference: FBC:Autogenerated

embryonic labral segment
type: Class
equivalent class: Class
  intersection of: labral segment
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: labral segment
subclass of: embryonic procephalic segment
definition: Any labral segment of the embryo.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000159
in subset: cur

Axiom
annotated source: embryonic labral segment
annotated property: definition
annotated target: Any labral segment of the embryo.
database_cross_reference: FBC:Autogenerated

embryonic antennal segment
type: Class
equivalent class: Class
  intersection of: antennal segment
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: antennal segment
subclass of: embryonic procephalic segment
definition: Any antennal segment of the embryo.
database_cross_reference: UBERON:6000160
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000160
in subset: cur

Axiom
annotated source: embryonic antennal segment
annotated property: definition
annotated target: Any antennal segment of the embryo.
database_cross_reference: FBC:Autogenerated

embryonic optic lobe primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: late extended germ band embryo
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: visual primordium
subclass of: Restriction
  on property: develops into
  some values from: larval optic anlage
definition: Primordium of the late extended germ band and closure embryo that gives rise to the embryonic/larval optic anlage. It corresponds to the middle region that develops from the visual primordium.
database_cross_reference: UBERON:6000186
has OBO namespace: fly_anatomy.ontology
id: FBbt:00000186
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic optic lobe primordium
annotated property: definition
annotated target: Primordium of the late extended germ band and closure embryo that gives rise to the embryonic/larval optic anlage. It corresponds to the middle region that develops from the visual primordium.
database_cross_reference: FBC:VH
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0151275
database_cross_reference: https://orcid.org/0000-0002-7073-9172

larval apodeme
type: Class
equivalent class: Class
  intersection of: apodeme
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: apodeme
subclass of: Restriction
  on property: part of
  some values from: larval integumentary system
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Apodeme that is part of the late embryo/larva. Apodemes are not a continuous structure, but are split into two halves. In the embryo, this break is visible laterally. In the larva, the dorsal and ventral halves in the thoracic and abdominal segments are staggered, with the dorsal part being posterior to the ventral one.
has exact synonym: embryonic/larval apodeme
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001005
in subset: cur

Axiom
annotated source: larval apodeme
annotated property: definition
annotated target: Apodeme that is part of the late embryo/larva. Apodemes are not a continuous structure, but are split into two halves. In the embryo, this break is visible laterally. In the larva, the dorsal and ventral halves in the thoracic and abdominal segments are staggered, with the dorsal part being posterior to the ventral one.
database_cross_reference: FBC:SPR
database_cross_reference: FlyBase:FBrf0089570

presumptive embryonic/larval nervous system
type: Class
subclass of: presumptive embryonic/larval system
definition: The sum of all the structures in the embryo that will develop into the embryonic/larval nervous system.
database_cross_reference: UBERON:6001055
has OBO namespace: fly_anatomy.ontology
has related synonym: embryonic nervous system
id: FBbt:00001055
in subset: cur
in subset: expressionslim flybase ribbon

Axiom
annotated source: presumptive embryonic/larval nervous system
annotated property: definition
annotated target: The sum of all the structures in the embryo that will develop into the embryonic/larval nervous system.
database_cross_reference: FlyBase:FBrf0031012

Axiom
annotated source: presumptive embryonic/larval nervous system
annotated property: hasRelatedSynonym
annotated target: embryonic nervous system
database_cross_reference: https://orcid.org/0000-0002-7073-9172

presumptive embryonic/larval central nervous system
type: Class
subclass of: presumptive embryonic/larval system
subclass of: Restriction
  on property: part of
  some values from: presumptive embryonic/larval nervous system
definition: The sum of all the structures in the embryo that will develop into the embryonic/larval central nervous system.
database_cross_reference: UBERON:6001056
has OBO namespace: fly_anatomy.ontology
has related synonym: embryonic central nervous system
id: FBbt:00001056
in subset: cur

Axiom
annotated source: presumptive embryonic/larval central nervous system
annotated property: definition
annotated target: The sum of all the structures in the embryo that will develop into the embryonic/larval central nervous system.
database_cross_reference: FlyBase:FBrf0031012

Axiom
annotated source: presumptive embryonic/larval central nervous system
annotated property: hasRelatedSynonym
annotated target: embryonic central nervous system
database_cross_reference: https://orcid.org/0000-0002-7073-9172

neurogenic region
type: Class
subclass of: developing embryonic structure
subclass of: Restriction
  on property: part of
  some values from: ectoderm
definition: Region that gives rise to the neuroblasts of the central nervous system (Bossing et al., 1996). An anterior region (procephalic neurogenic region) gives rise to the brain and a posterior, ventral region (ventral neuroectoderm) gives rise to the ventral nerve cord and gnathal ganglia (Bossing et al., 1996).
database_cross_reference: UBERON:0002346
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001057
in subset: cur

Axiom
annotated source: neurogenic region
annotated property: definition
annotated target: Region that gives rise to the neuroblasts of the central nervous system (Bossing et al., 1996). An anterior region (procephalic neurogenic region) gives rise to the brain and a posterior, ventral region (ventral neuroectoderm) gives rise to the ventral nerve cord and gnathal ganglia (Bossing et al., 1996).
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0090460
database_cross_reference: FlyBase:FBrf0098344

procephalic neurogenic region
type: Class
subclass of: neurogenic region
subclass of: Restriction
  on property: part of
  some values from: anterior ectoderm
subclass of: Restriction
  on property: part of
  some values from: embryonic head
definition: Tissue which becomes morphologically distinct shortly after cephalic furrow formation as two strips of about 80 enlarged cells which extend dorso-ventrally on either side of the developing head. It gives rise to neuroblasts of the brain.
has exact synonym: pregnathal neuroectoderm
has exact synonym: procephalic neuroectoderm
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001058
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: procephalic neurogenic region
annotated property: definition
annotated target: Tissue which becomes morphologically distinct shortly after cephalic furrow formation as two strips of about 80 enlarged cells which extend dorso-ventrally on either side of the developing head. It gives rise to neuroblasts of the brain.
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0090460

Axiom
annotated source: procephalic neurogenic region
annotated property: hasExactSynonym
annotated target: pregnathal neuroectoderm
database_cross_reference: FlyBase:FBrf0161020

Axiom
annotated source: procephalic neurogenic region
annotated property: hasExactSynonym
annotated target: procephalic neuroectoderm
database_cross_reference: FlyBase:FBrf0161020

visual primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: anterior ectoderm derivative
subclass of: Class
  intersection of: Restriction
    on property: develops into
    some values from: embryonic optic lobe primordium
  intersection of: Restriction
    on property: develops into
    some values from: early embryonic primordium of adult eye
  intersection of: Restriction
    on property: develops into
    some values from: Bolwig organ primordium
subclass of: Restriction
  on property: part of
  some values from: early extended germ band embryo
subclass of: Restriction
  on property: develops from
  some values from: visual anlage
definition: Primordium of the early extended germ band embryo that will give rise to the larval Bolwig organ, larval optic anlage and adult eye. It is a dorsoposterior strip of the embryonic procephalon that invaginates at stages 12-13. It can be subdivided into 4 different regions. The most anterior gives rise to the embryonic primordium of adult eye. Posterior to it, the anterior lip develops into the embryonic inner optic lobe primordium, that will give rise to the larval inner optic anlage. Posteriorly, the posterior lip develops into the embryonic outer optic lobe primordium, that will give rise to the larval outer optic anlage. The most posterior region will develop into the Bolwig organ primordium.
database_cross_reference: UBERON:6001059
has exact synonym: optic lobe placode
has exact synonym: optic lobe primordium
has OBO namespace: fly_anatomy.ontology
has related synonym: P2 VisSys
id: FBbt:00001059
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: visual primordium
annotated property: definition
annotated target: Primordium of the early extended germ band embryo that will give rise to the larval Bolwig organ, larval optic anlage and adult eye. It is a dorsoposterior strip of the embryonic procephalon that invaginates at stages 12-13. It can be subdivided into 4 different regions. The most anterior gives rise to the embryonic primordium of adult eye. Posterior to it, the anterior lip develops into the embryonic inner optic lobe primordium, that will give rise to the larval inner optic anlage. Posteriorly, the posterior lip develops into the embryonic outer optic lobe primordium, that will give rise to the larval outer optic anlage. The most posterior region will develop into the Bolwig organ primordium.
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0151275

Axiom
annotated source: visual primordium
annotated property: hasExactSynonym
annotated target: optic lobe placode
database_cross_reference: FlyBase:FBrf0151275

Axiom
annotated source: visual primordium
annotated property: hasRelatedSynonym
annotated target: P2 VisSys
database_cross_reference: https://orcid.org/0000-0002-7073-9172

embryonic brain
type: Class
subclass of: supraesophageal ganglion
subclass of: brain
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: presumptive embryonic/larval central nervous system
subclass of: Restriction
  on property: develops from
  some values from: procephalic neurogenic region
definition: Brain of the embryo, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Crews, 2019). It develops from the procephalic neurogenic region (Urbach and Technau, 2003).
database_cross_reference: UBERON:6001060
database_cross_reference: VFB:FBbt_00001060
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001060
in subset: cur

Axiom
annotated source: embryonic brain
annotated property: definition
annotated target: Brain of the embryo, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Crews, 2019). It develops from the procephalic neurogenic region (Urbach and Technau, 2003).
database_cross_reference: FlyBase:FBrf0161020
database_cross_reference: FlyBase:FBrf0244240

ventral neurectoderm
type: Class
subclass of: neurogenic region
subclass of: epithelium
subclass of: Restriction
  on property: part of
  some values from: ventral ectoderm
definition: The ventrally/medially located ectodermal region of the trunk from which neuroblasts delaminate to form the ventral nerve cord and gnathal ganglia. This region becomes distinct during stage 8 when its cells become enlarged compared to those in the adjacent dorsal ectoderm.
has alternative id: FBbt:00000113
has exact synonym: P2 VenEc
has exact synonym: VenEc
has exact synonym: vNR
has exact synonym: ventral neurogenic region
has OBO namespace: fly_anatomy.ontology
has related synonym: neurectoderm
has related synonym: neuroectoderm
id: FBbt:00001061
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: ventral neurectoderm
annotated property: definition
annotated target: The ventrally/medially located ectodermal region of the trunk from which neuroblasts delaminate to form the ventral nerve cord and gnathal ganglia. This region becomes distinct during stage 8 when its cells become enlarged compared to those in the adjacent dorsal ectoderm.
database_cross_reference: FlyBase:FBrf0076117
database_cross_reference: FlyBase:FBrf0089570

Axiom
annotated source: ventral neurectoderm
annotated property: hasExactSynonym
annotated target: vNR
database_cross_reference: FlyBase:FBrf0090460

Axiom
annotated source: ventral neurectoderm
annotated property: hasExactSynonym
annotated target: ventral neurogenic region
database_cross_reference: FlyBase:FBrf0090460

embryonic glioblast
type: Class
equivalent class: Class
  intersection of: glioblast
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: embryonic neuroblast
subclass of: glioblast
definition: Glioblast of the embryo.
database_cross_reference: VFB:FBbt_00001244
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001244
in subset: cur

Axiom
annotated source: embryonic glioblast
annotated property: definition
annotated target: Glioblast of the embryo.
database_cross_reference: FlyBase:FBrf0105240

larval glial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: glial cell
subclass of: Restriction
  on property: part of
  some values from: larval nervous system
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Glial cell of the late embryo/larva.
database_cross_reference: VFB:FBbt_00001251
has exact synonym: embryonic/larval glial cell
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001251
in subset: cur

Axiom
annotated source: larval glial cell
annotated property: definition
annotated target: Glial cell of the late embryo/larva.
database_cross_reference: FlyBase:FBrf0050373
database_cross_reference: FlyBase:FBrf0053160
database_cross_reference: FlyBase:FBrf0054242
database_cross_reference: FlyBase:FBrf0090460
database_cross_reference: FlyBase:FBrf0098344
database_cross_reference: FlyBase:FBrf0105240
database_cross_reference: FlyBase:FBrf0205499
database_cross_reference: FlyBase:FBrf0214261

CNS glial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: part of
    some values from: central nervous system
subclass of: glial cell
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: Glial cell of the central nervous system.
database_cross_reference: VFB:FBbt_00001256
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001256
in subset: cur

Axiom
annotated source: CNS glial cell
annotated property: definition
annotated target: Glial cell of the central nervous system.
database_cross_reference: FlyBase:FBrf0206543

cell body glial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: part of
    some values from: cell body rind of the central nervous system
subclass of: CNS glial cell
subclass of: Restriction
  on property: part of
  some values from: cell body rind of the central nervous system
definition: Glial cell with a nucleus amongst the neuronal cell bodies in the cell body rind. It is irregularly shaped, with processes that enclose the neuronal cell bodies.
database_cross_reference: VFB:FBbt_00001297
has exact synonym: CBG
has exact synonym: cell body-associated glial cell
has exact synonym: cortex associated CNS glial cell
has exact synonym: cortex glial cell
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001297
in subset: cur
comment: Glial cells associated with axonal tracts (such as those associated with nerve roots) are excluded from this class of glial cells (Ito et al., 1995). Modeled as 'part of' their 'cell body rind' regions, though in practice some cell body glia have small projections into the neuropil - https://orcid.org/0000-0002-1373-1705.

Axiom
annotated source: cell body glial cell
annotated property: definition
annotated target: Glial cell with a nucleus amongst the neuronal cell bodies in the cell body rind. It is irregularly shaped, with processes that enclose the neuronal cell bodies.
database_cross_reference: FlyBase:FBrf0082171
database_cross_reference: FlyBase:FBrf0214261

Axiom
annotated source: cell body glial cell
annotated property: hasExactSynonym
annotated target: CBG
database_cross_reference: FlyBase:FBrf0082171

Axiom
annotated source: cell body glial cell
annotated property: hasExactSynonym
annotated target: cell body-associated glial cell
database_cross_reference: FlyBase:FBrf0214261

Axiom
annotated source: cell body glial cell
annotated property: hasExactSynonym
annotated target: cortex glial cell
database_cross_reference: FlyBase:FBrf0214261

embryonic/larval cell body glial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: part of
    some values from: cell body rind of larval central nervous system
subclass of: cell body glial cell
subclass of: embryonic/larval lateral glial cell
subclass of: Restriction
  on property: part of
  some values from: cell body rind of larval central nervous system
definition: Glial cell located amongst neuronal cell bodies in the cell body rind of the embryonic/larval central nervous system.
database_cross_reference: VFB:FBbt_00001298
has exact synonym: embryonic/larval cortex glial cell
has exact synonym: larval CBG
has OBO namespace: fly_anatomy.ontology
has related synonym: CoG
id: FBbt:00001298
in subset: cur

Axiom
annotated source: embryonic/larval cell body glial cell
annotated property: definition
annotated target: Glial cell located amongst neuronal cell bodies in the cell body rind of the embryonic/larval central nervous system.
database_cross_reference: FlyBase:FBrf0082171
database_cross_reference: FlyBase:FBrf0214261
database_cross_reference: FlyBase:FBrf0237238

Axiom
annotated source: embryonic/larval cell body glial cell
annotated property: hasExactSynonym
annotated target: embryonic/larval cortex glial cell
database_cross_reference: FlyBase:FBrf0214261

Axiom
annotated source: embryonic/larval cell body glial cell
annotated property: hasExactSynonym
annotated target: larval CBG
database_cross_reference: FlyBase:FBrf0082171

PNS glial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: part of
    some values from: peripheral nervous system
subclass of: glial cell
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
definition: Glial cell that is part of the peripheral nervous system.
database_cross_reference: VFB:FBbt_00001320
has exact synonym: peripheral glial cell
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001320
in subset: cur

Axiom
annotated source: PNS glial cell
annotated property: definition
annotated target: Glial cell that is part of the peripheral nervous system.
database_cross_reference: FBC:SPR

embryonic neuroblast
type: Class
equivalent class: Class
  intersection of: neuroblast
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: developing embryonic structure
subclass of: neuroblast
subclass of: Restriction
  on property: part of
  some values from: presumptive embryonic/larval nervous system
definition: Any neuroblast of the embryo.
database_cross_reference: VFB:FBbt_00001332
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001332
in subset: cur

Axiom
annotated source: embryonic neuroblast
annotated property: definition
annotated target: Any neuroblast of the embryo.
database_cross_reference: FlyBase:FBrf0055900

procephalic neuroblast
type: Class
subclass of: neuroblast
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: develops from
  some values from: procephalic neurogenic region
definition: Neuroblast of one of the three procephalic regions, protocerebrum, deutocerebrum and tritocerebrum, which form the supraesophageal ganglion of the brain (Urbach et al., 2003). These neuroblasts derive from the procephalic neurogenic region (Urbach et al., 2003).
database_cross_reference: VFB:FBbt_00001333
has exact synonym: neuroblast of supraesophageal ganglion
has narrow synonym: brain neuroblast
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001333
in subset: cur

Axiom
annotated source: procephalic neuroblast
annotated property: definition
annotated target: Neuroblast of one of the three procephalic regions, protocerebrum, deutocerebrum and tritocerebrum, which form the supraesophageal ganglion of the brain (Urbach et al., 2003). These neuroblasts derive from the procephalic neurogenic region (Urbach et al., 2003).
database_cross_reference: FlyBase:FBrf0161021

protocerebral neuroblast
type: Class
equivalent class: Class
  intersection of: neuroblast
  intersection of: Restriction
    on property: part of
    some values from: protocerebrum
subclass of: procephalic neuroblast
subclass of: Restriction
  on property: part of
  some values from: protocerebrum
definition: A neuroblast located in the protocerebrum. None of these are serial homologues of neuroblasts found in the thoracic neuromeres (Urbach et al., 2016).
database_cross_reference: VFB:FBbt_00001334
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001334
in subset: cur
comment: In the embryo, individual neuroblasts are named according to their position relative to major morphological features (cephalic furrow, invaginating foregut, dorsal and ventral midline, their relative position with respect to each other, their time of segregation and their expression of markers) (Urbach et al., 2003).

Axiom
annotated source: protocerebral neuroblast
annotated property: definition
annotated target: A neuroblast located in the protocerebrum. None of these are serial homologues of neuroblasts found in the thoracic neuromeres (Urbach et al., 2016).
database_cross_reference: FlyBase:FBrf0089217
database_cross_reference: FlyBase:FBrf0161021
database_cross_reference: FlyBase:FBrf0232096

deutocerebral neuroblast
type: Class
equivalent class: Class
  intersection of: neuroblast
  intersection of: Restriction
    on property: part of
    some values from: deutocerebrum
subclass of: procephalic neuroblast
subclass of: Restriction
  on property: part of
  some values from: deutocerebrum
definition: A neuroblast located in the deutocerebrum. Some of these are serial homologues of neuroblasts found in the thoracic neuromeres (Urbach et al., 2016).
database_cross_reference: VFB:FBbt_00001353
has exact synonym: deuterocerebral neuroblast
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001353
in subset: cur
comment: In the embryo, individual neuroblasts are named according to their position relative to major morphological features (cephalic furrow, invaginating foregut, dorsal and ventral midline, their relative position with respect to each other, their time of segregation and their expression of markers) (Urbach et al., 2003).

Axiom
annotated source: deutocerebral neuroblast
annotated property: definition
annotated target: A neuroblast located in the deutocerebrum. Some of these are serial homologues of neuroblasts found in the thoracic neuromeres (Urbach et al., 2016).
database_cross_reference: FlyBase:FBrf0089217
database_cross_reference: FlyBase:FBrf0161021
database_cross_reference: FlyBase:FBrf0232096

supraesophageal ganglion neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: has soma location
    some values from: supraesophageal ganglion
subclass of: CNS neuron
subclass of: Restriction
  on property: has soma location
  some values from: supraesophageal ganglion
definition: Any neuron (FBbt:00005106) that has its soma located in some supraesophageal ganglion (FBbt:00003626).
database_cross_reference: VFB:FBbt_00001366
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001366
in subset: cur

Axiom
annotated source: supraesophageal ganglion neuron
annotated property: definition
annotated target: Any neuron (FBbt:00005106) that has its soma located in some supraesophageal ganglion (FBbt:00003626).
database_cross_reference: FBC:Autogenerated

larval neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: larval nervous system
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Neuron that is part of the larval nervous system. Neurons with functional roles in the larva are born during the embryonic phase of neurogenesis and further neurons, with adult-specific roles, are born during the postembryonic phase, which begins during larval development (Lacin and Truman, 2016).
database_cross_reference: VFB:FBbt_00001446
has exact synonym: embryonic/larval neuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001446
in subset: cur
comment: This includes immature secondary neurons that are found in the larva - https://orcid.org/0000-0002-1373-1705.

Axiom
annotated source: larval neuron
annotated property: definition
annotated target: Neuron that is part of the larval nervous system. Neurons with functional roles in the larva are born during the embryonic phase of neurogenesis and further neurons, with adult-specific roles, are born during the postembryonic phase, which begins during larval development (Lacin and Truman, 2016).
database_cross_reference: FlyBase:FBrf0090460
database_cross_reference: FlyBase:FBrf0098344
database_cross_reference: FlyBase:FBrf0231327

embryonic imaginal tissue
type: Class
equivalent class: Class
  intersection of: imaginal tissue
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: developing embryonic structure
subclass of: imaginal tissue
definition: Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993).
database_cross_reference: UBERON:6001648
has exact synonym: embryonic imaginal precursor
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001648
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic imaginal tissue
annotated property: definition
annotated target: Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993).
database_cross_reference: FlyBase:FBrf0064789

imaginal disc primordium
type: Class
subclass of: embryonic imaginal tissue
subclass of: primordium
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: ventral epidermis primordium
subclass of: Restriction
  on property: develops into
  some values from: imaginal disc
definition: Population of contiguous, morphologically distinct cells of the embryo that will proliferate to form an imaginal disc in the larva. During early embryogenesis the precursor is part of the epithelial sheet before segregating from the epithelial sheet by late embryogenesis (Cohen, 1993).
database_cross_reference: UBERON:6001649
has OBO namespace: fly_anatomy.ontology
has related synonym: imaginal disc specific anlage
id: FBbt:00001649
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: imaginal disc primordium
annotated property: definition
annotated target: Population of contiguous, morphologically distinct cells of the embryo that will proliferate to form an imaginal disc in the larva. During early embryogenesis the precursor is part of the epithelial sheet before segregating from the epithelial sheet by late embryogenesis (Cohen, 1993).
database_cross_reference: FBC:SPR
database_cross_reference: FlyBase:FBrf0064789

eye-antennal disc primordium
type: Class
subclass of: imaginal disc primordium
subclass of: Restriction
  on property: part of
  some values from: embryonic antennal segment
subclass of: Restriction
  on property: part of
  some values from: late extended germ band embryo
subclass of: Restriction
  on property: develops into
  some values from: eye-antennal disc
definition: Primordium from which the eye-antennal disc develops.
database_cross_reference: UBERON:6001652
has OBO namespace: fly_anatomy.ontology
has related synonym: eye-antennal disc specific anlage
id: FBbt:00001652
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: eye-antennal disc primordium
annotated property: definition
annotated target: Primordium from which the eye-antennal disc develops.
database_cross_reference: FBC:SPR

larva
type: Class
subclass of: BFO_0000002
subclass of: organism
subclass of: Restriction
  on property: develops from
  some values from: embryo
database_cross_reference: UBERON:0002548
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001727
in subset: FB gloss
in subset: cur
in subset: larval OF

larval tagma
type: Class
equivalent class: Class
  intersection of: tagma
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: tagma
subclass of: Restriction
  on property: part of
  some values from: larva
definition: Any tagma of the larva.
database_cross_reference: UBERON:6001728
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001728
in subset: cur

Axiom
annotated source: larval tagma
annotated property: definition
annotated target: Any tagma of the larva.
database_cross_reference: FBC:Autogenerated

larval segment
type: Class
equivalent class: Class
  intersection of: segment
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: BFO_0000002
subclass of: segment
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: develops from
  some values from: embryonic segment
definition: Any segment of the larva.
database_cross_reference: UBERON:6001729
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001729
in subset: cur
in subset: larval OF

Axiom
annotated source: larval segment
annotated property: definition
annotated target: Any segment of the larva.
database_cross_reference: FBC:Autogenerated

larval head
type: Class
equivalent class: Class
  intersection of: head
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: head
subclass of: larval tagma
definition: Any head of the larva.
database_cross_reference: UBERON:6001730
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001730
in subset: cur
in subset: larval OF

Axiom
annotated source: larval head
annotated property: definition
annotated target: Any head of the larva.
database_cross_reference: FBC:Autogenerated

larval ocular segment
type: Class
equivalent class: Class
  intersection of: ocular segment
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: ocular segment
subclass of: larval procephalic segment
definition: Any ocular segment of the larva.
database_cross_reference: UBERON:6001731
has OBO namespace: fly_anatomy.ontology
has related synonym: larval acron
id: FBbt:00001731
in subset: cur

Axiom
annotated source: larval ocular segment
annotated property: definition
annotated target: Any ocular segment of the larva.
database_cross_reference: FBC:Autogenerated

larval head segment
type: Class
equivalent class: Class
  intersection of: head segment
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: head segment
subclass of: larval segment
subclass of: Restriction
  on property: part of
  some values from: larval head
definition: Any head segment of the larva.
database_cross_reference: UBERON:6001732
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001732
in subset: cur
in subset: larval OF

Axiom
annotated source: larval head segment
annotated property: definition
annotated target: Any head segment of the larva.
database_cross_reference: FlyBase:FBrf0075072

larval procephalic segment
type: Class
equivalent class: Class
  intersection of: procephalic segment
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: procephalic segment
subclass of: larval head segment
definition: Any procephalic segment of the larva.
database_cross_reference: UBERON:6001733
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001733
in subset: cur
in subset: larval OF

Axiom
annotated source: larval procephalic segment
annotated property: definition
annotated target: Any procephalic segment of the larva.
database_cross_reference: FBC:Autogenerated

larval labral segment
type: Class
equivalent class: Class
  intersection of: labral segment
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: labral segment
subclass of: larval procephalic segment
definition: Any labral segment of the larva.
database_cross_reference: UBERON:6001734
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001734
in subset: cur
in subset: larval OF

Axiom
annotated source: larval labral segment
annotated property: definition
annotated target: Any labral segment of the larva.
database_cross_reference: FBC:Autogenerated

larval antennal segment
type: Class
equivalent class: Class
  intersection of: antennal segment
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: antennal segment
subclass of: larval procephalic segment
definition: Any antennal segment of the larva.
database_cross_reference: UBERON:6001735
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001735
in subset: cur
in subset: larval OF

Axiom
annotated source: larval antennal segment
annotated property: definition
annotated target: Any antennal segment of the larva.
database_cross_reference: FBC:Autogenerated

larval imaginal tissue
type: Class
equivalent class: Class
  intersection of: imaginal tissue
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: BFO_0000002
subclass of: imaginal tissue
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: develops from
  some values from: embryonic imaginal tissue
definition: Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis.
database_cross_reference: UBERON:6001760
has exact synonym: embryonic/larval imaginal precursor
has exact synonym: larval imaginal precursor
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001760
in subset: cur

Axiom
annotated source: larval imaginal tissue
annotated property: definition
annotated target: Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis.
database_cross_reference: FlyBase:FBrf0064789

imaginal disc
type: Class
subclass of: larval imaginal tissue
subclass of: multi-tissue structure
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: develops from
  some values from: imaginal disc primordium
definition: A sac shaped epithelial structure in the larva that gives rise to part of the adult integumentary system. One side of the sac consists of peripodial epithelium, the other of columnar epithelium. A single anterior-posterior compartment boundary bisects both peripodial membrane and columnar epithelium. Cells do not cross this boundary during growth and development of the disc.
database_cross_reference: UBERON:0000939
has OBO namespace: fly_anatomy.ontology
has related synonym: imaginal disk
id: FBbt:00001761
in subset: FB gloss
in subset: cur

Axiom
annotated source: imaginal disc
annotated property: definition
annotated target: A sac shaped epithelial structure in the larva that gives rise to part of the adult integumentary system. One side of the sac consists of peripodial epithelium, the other of columnar epithelium. A single anterior-posterior compartment boundary bisects both peripodial membrane and columnar epithelium. Cells do not cross this boundary during growth and development of the disc.
database_cross_reference: FBC:GG

eye-antennal disc
type: Class
subclass of: imaginal disc
subclass of: Restriction
  on property: develops from
  some values from: eye-antennal disc primordium
definition: Imaginal disc that, in the adults, gives rise to the eye, antenna, head capsule (including all bristles and external membranes) and the maxillary palps (Cohen, 1993).
database_cross_reference: UBERON:6001766
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001766
in subset: EmbDevSlim
in subset: cur
comment: Figure 12 from Cohen (1993, Bate, Martinez Arias, 1993: 747--841) provides a fate map of the eye-antennal disc.

Axiom
annotated source: eye-antennal disc
annotated property: definition
annotated target: Imaginal disc that, in the adults, gives rise to the eye, antenna, head capsule (including all bristles and external membranes) and the maxillary palps (Cohen, 1993).
database_cross_reference: FlyBase:FBrf0064789

eye disc
type: Class
subclass of: imaginal disc
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: eye-antennal disc
subclass of: Restriction
  on property: develops from
  some values from: late embryonic primordium of adult eye
definition: Anterior, bulbous portion of the eye-antennal disc that gives rise to the eye as well as contributing to the head capsule (Cohen, 1993).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001768
in subset: cur
comment: Figure 12 from Cohen (1993, Bate, Martinez Arias, 1993: 747--841) provides a fate map of the eye-antennal disc.

Axiom
annotated source: eye disc
annotated property: definition
annotated target: Anterior, bulbous portion of the eye-antennal disc that gives rise to the eye as well as contributing to the head capsule (Cohen, 1993).
database_cross_reference: FlyBase:FBrf0064789

larval digestive system
type: Class
equivalent class: Class
  intersection of: digestive system
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: digestive system
subclass of: Restriction
  on property: part of
  some values from: larva
definition: Any digestive system of the larva.
has alternative id: FBbt:00005764
database_cross_reference: UBERON:6001842
has exact synonym: embryonic/larval digestive system
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001842
in subset: cur

Axiom
annotated source: larval digestive system
annotated property: definition
annotated target: Any digestive system of the larva.
database_cross_reference: FlyBase:FBrf0007733
database_cross_reference: FlyBase:FBrf0064792

larval nervous system
type: Class
equivalent class: Class
  intersection of: nervous system
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: nervous system
subclass of: Restriction
  on property: part of
  some values from: larva
definition: Nervous system of the embryo/larva.
has alternative id: FBbt:00005719
database_cross_reference: UBERON:6001911
database_cross_reference: VFB:FBbt_00001911
has exact synonym: embryonic/larval nervous system
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001911
in subset: cur

Axiom
annotated source: larval nervous system
annotated property: definition
annotated target: Nervous system of the embryo/larva.
database_cross_reference: FlyBase:FBrf0045359
database_cross_reference: FlyBase:FBrf0075072
database_cross_reference: FlyBase:FBrf0105282

larval neuromere
type: Class
equivalent class: Class
  intersection of: neuromere
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: neuromere
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: larval segment
  intersection of: Restriction
    on property: part of
    some values from: larval central nervous system
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Neuromere of the larval nervous system.
database_cross_reference: VFB:FBbt_00001912
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001912
in subset: cur

Axiom
annotated source: larval neuromere
annotated property: definition
annotated target: Neuromere of the larval nervous system.
database_cross_reference: FlyBase:FBrf0047815
database_cross_reference: FlyBase:FBrf0084032
database_cross_reference: FlyBase:FBrf0089217
database_cross_reference: FlyBase:FBrf0105282

larval central nervous system
type: Class
equivalent class: Class
  intersection of: central nervous system
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: central nervous system
subclass of: Restriction
  on property: part of
  some values from: larval nervous system
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Central nervous system of the embryo/larva.
database_cross_reference: UBERON:6001919
database_cross_reference: VFB:FBbt_00001919
has exact synonym: embryonic/larval CNS
has exact synonym: embryonic/larval central nervous system
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001919
in subset: cur
in subset: larval OF

Axiom
annotated source: larval central nervous system
annotated property: definition
annotated target: Central nervous system of the embryo/larva.
database_cross_reference: FBC:SPR

larval brain
type: Class
equivalent class: Class
  intersection of: brain
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: supraesophageal ganglion
subclass of: brain
subclass of: anterior ectoderm derivative
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: larval head
  intersection of: Restriction
    on property: part of
    some values from: larval central nervous system
subclass of: Restriction
  on property: overlaps
  some values from: larva
subclass of: Restriction
  on property: develops from
  some values from: embryonic brain
definition: Supraesophageal ganglion of the late embryo or larva, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019).
database_cross_reference: UBERON:6001920
database_cross_reference: VFB:FBbt_00001920
has exact synonym: embryonic/larval SPG
has exact synonym: embryonic/larval brain
has exact synonym: embryonic/larval supraesophageal complex
has exact synonym: embryonic/larval supraesophageal ganglion
has exact synonym: larval SPG
has exact synonym: larval cerebral ganglion
has exact synonym: larval supraesophageal ganglion
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001920
in subset: BrainName
in subset: cur
in subset: larval OF

Axiom
annotated source: larval brain
annotated property: definition
annotated target: Supraesophageal ganglion of the late embryo or larva, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019).
database_cross_reference: FlyBase:FBrf0161020
database_cross_reference: FlyBase:FBrf0225812
database_cross_reference: FlyBase:FBrf0244240

Axiom
annotated source: larval brain
annotated property: hasExactSynonym
annotated target: embryonic/larval supraesophageal complex
database_cross_reference: FlyBase:FBrf0225812

larval protocerebrum
type: Class
equivalent class: Class
  intersection of: protocerebrum
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuromere
subclass of: protocerebrum
subclass of: Restriction
  on property: part of
  some values from: larval supraesophageal zone
subclass of: Restriction
  on property: overlaps
  some values from: larval ocular segment
subclass of: Restriction
  on property: overlaps
  some values from: larval labral segment
definition: Protocerebrum of the embryo/larva.
database_cross_reference: UBERON:6001925
database_cross_reference: VFB:FBbt_00001925
database_cross_reference: larvalbrain_neuropil:392
database_cross_reference: larvalbrain_neuropil:570
has exact synonym: embryonic/larval protocerebrum
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001925
in subset: cur
in subset: larval OF

Axiom
annotated source: larval protocerebrum
annotated property: definition
annotated target: Protocerebrum of the embryo/larva.
database_cross_reference: FBC:SPR

embryonic/larval optic lobe
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part of
  some values from: larval protocerebrum
definition: Region of the embryonic or larval brain that contains the neuroepithelial cells that will give rise to the adult optic lobe, and the larval optic neuropil that processes visual information in the larva.
database_cross_reference: VFB:FBbt_00001930
database_cross_reference: larvalbrain_neuropil:391
database_cross_reference: larvalbrain_neuropil:569
has exact synonym: larval optic lobe
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001930
in subset: cur

Axiom
annotated source: embryonic/larval optic lobe
annotated property: definition
annotated target: Region of the embryonic or larval brain that contains the neuroepithelial cells that will give rise to the adult optic lobe, and the larval optic neuropil that processes visual information in the larva.
database_cross_reference: FlyBase:FBrf0052913
database_cross_reference: FlyBase:FBrf0064800
database_cross_reference: FlyBase:FBrf0215208

larval deutocerebrum
type: Class
equivalent class: Class
  intersection of: larval neuromere
  intersection of: Restriction
    on property: part of
    some values from: antennal segment
subclass of: larval neuromere
subclass of: deutocerebrum
subclass of: Restriction
  on property: part of
  some values from: larval antennal segment
subclass of: Restriction
  on property: part of
  some values from: larval central brain
subclass of: Restriction
  on property: part of
  some values from: larval supraesophageal zone
definition: Deutocerebrum of the embryo/larva.
database_cross_reference: VFB:FBbt_00001957
database_cross_reference: larvalbrain_neuropil:337
database_cross_reference: larvalbrain_neuropil:515
has exact synonym: embryonic/larval deuterocerebrum
has exact synonym: embryonic/larval deutocerebrum
has exact synonym: larval deuterocerebrum
has OBO namespace: fly_anatomy.ontology
id: FBbt:00001957
in subset: cur
in subset: larval OF

Axiom
annotated source: larval deutocerebrum
annotated property: definition
annotated target: Deutocerebrum of the embryo/larva.
database_cross_reference: FBC:SPR

larval sense organ
type: Class
equivalent class: Class
  intersection of: sense organ
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: sense organ
subclass of: Restriction
  on property: part of
  some values from: larva
definition: Any sense organ of the larva.
database_cross_reference: UBERON:6002639
database_cross_reference: VFB:FBbt_00002639
has exact synonym: embryonic/larval sense organ
has OBO namespace: fly_anatomy.ontology
id: FBbt:00002639
in subset: cur

Axiom
annotated source: larval sense organ
annotated property: definition
annotated target: Any sense organ of the larva.
database_cross_reference: FBC:Autogenerated

larval ocular segment sense organ
type: Class
equivalent class: Class
  intersection of: larval sense organ
  intersection of: Restriction
    on property: part of
    some values from: ocular segment
subclass of: embryonic/larval head sense organ
subclass of: Restriction
  on property: part of
  some values from: larval ocular segment
definition: Any larval sense organ (FBbt:00002639) that is part of some ocular segment (FBbt:00000005).
database_cross_reference: UBERON:6002642
database_cross_reference: VFB:FBbt_00002642
has narrow synonym: embryonic/larval ocular segment sensillum
has OBO namespace: fly_anatomy.ontology
id: FBbt:00002642
in subset: cur

Axiom
annotated source: larval ocular segment sense organ
annotated property: definition
annotated target: Any larval sense organ (FBbt:00002639) that is part of some ocular segment (FBbt:00000005).
database_cross_reference: FBC:Autogenerated

embryonic/larval labral segment sense organ
type: Class
equivalent class: Class
  intersection of: larval sense organ
  intersection of: Restriction
    on property: part of
    some values from: labral segment
subclass of: embryonic/larval head sense organ
subclass of: Restriction
  on property: part of
  some values from: larval labral segment
definition: Any larval sense organ (FBbt:00002639) that is part of some labral segment (FBbt:00000008).
has alternative id: FBbt:00002650
database_cross_reference: VFB:FBbt_00002649
has exact synonym: larval labral segment sense organ
has OBO namespace: fly_anatomy.ontology
id: FBbt:00002649
in subset: cur

Axiom
annotated source: embryonic/larval labral segment sense organ
annotated property: definition
annotated target: Any larval sense organ (FBbt:00002639) that is part of some labral segment (FBbt:00000008).
database_cross_reference: FBC:Autogenerated

larval antennal segment sense organ
type: Class
equivalent class: Class
  intersection of: larval sense organ
  intersection of: Restriction
    on property: part of
    some values from: antennal segment
subclass of: antennal sense organ
subclass of: embryonic/larval head sense organ
subclass of: Restriction
  on property: part of
  some values from: larval antennal segment
definition: Any larval sense organ (FBbt:00002639) that is part of some antennal segment (FBbt:00000009).
database_cross_reference: VFB:FBbt_00002654
has narrow synonym: embryonic/larval antennal segment sensillum
has OBO namespace: fly_anatomy.ontology
id: FBbt:00002654
in subset: cur

Axiom
annotated source: larval antennal segment sense organ
annotated property: definition
annotated target: Any larval sense organ (FBbt:00002639) that is part of some antennal segment (FBbt:00000009).
database_cross_reference: FBC:Autogenerated

alimentary canal
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part of
  some values from: digestive system
definition: The entire anatomical structure through which food and its digestion products are ingested, digested and excreted. At its anterior and posterior ends this includes structures that are not foregut or hindgut.
database_cross_reference: UBERON:0001555
has OBO namespace: fly_anatomy.ontology
id: FBbt:00003125
in subset: cur

Axiom
annotated source: alimentary canal
annotated property: definition
annotated target: The entire anatomical structure through which food and its digestion products are ingested, digested and excreted. At its anterior and posterior ends this includes structures that are not foregut or hindgut.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

supraesophageal ganglion
type: Class
subclass of: ganglion
subclass of: Restriction
  on property: part of
  some values from: brain
definition: The pre-oral neuropils of the brain located above and some of it below the esophagus, comprising three fused ganglia (protocerebrum, deutocerebrum, and tritocerebrum) in the head.
database_cross_reference: UBERON:6003626
database_cross_reference: VFB:FBbt_00003626
has OBO namespace: fly_anatomy.ontology
has related synonym: SPG
id: FBbt:00003626
in subset: BrainName
in subset: cur
comment: In the adult, this region is referred to as cerebral ganglia (Ito et al., 2014).

Axiom
annotated source: supraesophageal ganglion
annotated property: definition
annotated target: The pre-oral neuropils of the brain located above and some of it below the esophagus, comprising three fused ganglia (protocerebrum, deutocerebrum, and tritocerebrum) in the head.
database_cross_reference: FlyBase:FBrf0224194

protocerebrum
type: Class
subclass of: neuromere
subclass of: Restriction
  on property: part of
  some values from: supraesophageal zone
subclass of: Restriction
  on property: overlaps
  some values from: ocular segment
subclass of: Restriction
  on property: overlaps
  some values from: labral segment
definition: The most anterior neuromere of the central nervous system, developing from neuroblasts of the labral and ocular segments (Urbach and Technau, 2003; Ito et al., 2014). The protocerebrum comprises many discrete neuropil regions including the central complex and mushroom bodies (Ito et al., 2014).
database_cross_reference: UBERON:6003627
database_cross_reference: VFB:FBbt_00003627
has exact synonym: PR
has exact synonym: protocerebral neuromere
has OBO namespace: fly_anatomy.ontology
id: FBbt:00003627
in subset: cur
comment: Urbach and Technau (2003) divide the protocerebrum into labral and ocular neuromeres.

Axiom
annotated source: protocerebrum
annotated property: definition
annotated target: The most anterior neuromere of the central nervous system, developing from neuroblasts of the labral and ocular segments (Urbach and Technau, 2003; Ito et al., 2014). The protocerebrum comprises many discrete neuropil regions including the central complex and mushroom bodies (Ito et al., 2014).
database_cross_reference: FlyBase:FBrf0161020
database_cross_reference: FlyBase:FBrf0224194

Axiom
annotated source: protocerebrum
annotated property: hasExactSynonym
annotated target: PR
database_cross_reference: FlyBase:FBrf0224194

Axiom
annotated source: protocerebrum
annotated property: hasExactSynonym
annotated target: protocerebral neuromere
database_cross_reference: FlyBase:FBrf0092819

intrinsic neuron
type: Class
subclass of: local neuron
definition: Neuron of the central nervous system that arborizes exclusively within a given neuropil domain, ipsilaterally or bilaterally.
has alternative id: FBbt:00005126
database_cross_reference: VFB:FBbt_00003664
has OBO namespace: fly_anatomy.ontology
has related synonym: local interneuron
id: FBbt:00003664
in subset: cur

Axiom
annotated source: intrinsic neuron
annotated property: definition
annotated target: Neuron of the central nervous system that arborizes exclusively within a given neuropil domain, ipsilaterally or bilaterally.
database_cross_reference: FBC:SPR
database_cross_reference: FlyBase:FBrf0205263
database_cross_reference: FlyBase:FBrf0210154
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: intrinsic neuron
annotated property: hasRelatedSynonym
annotated target: local interneuron
database_cross_reference: FlyBase:FBrf0210154

mushroom body calyx
type: Class
subclass of: synaptic neuropil domain
subclass of: mushroom body neuropil subdivision
definition: A synaptic neuropil domain containing dendrites of Kenyon cells and receiving sensory interneuron afferents, mainly from the antennal lobes (Ito et al., 2014; Saumweber et al., 2018). It is located on the posterior side of the brain, close to the cortex where the cell bodies of the Kenyon cells are located (Lee et al., 1999; Saumweber et al., 2018). The peduncle extends anteriorly from the calyx to the base of the lobes (Ito et al., 2014; Saumweber et al., 2018).
database_cross_reference: VFB:FBbt_00003685
has exact synonym: CA
has exact synonym: calyx of corpora pedunculata
has exact synonym: calyx of mushroom body
has narrow synonym: main calyx
has OBO namespace: fly_anatomy.ontology
has related synonym: calyx
id: FBbt:00003685
in subset: BrainName
in subset: cur
in subset: larval OF

Axiom
annotated source: mushroom body calyx
annotated property: definition
annotated target: A synaptic neuropil domain containing dendrites of Kenyon cells and receiving sensory interneuron afferents, mainly from the antennal lobes (Ito et al., 2014; Saumweber et al., 2018). It is located on the posterior side of the brain, close to the cortex where the cell bodies of the Kenyon cells are located (Lee et al., 1999; Saumweber et al., 2018). The peduncle extends anteriorly from the calyx to the base of the lobes (Ito et al., 2014; Saumweber et al., 2018).
database_cross_reference: FlyBase:FBrf0111409
database_cross_reference: FlyBase:FBrf0224194
database_cross_reference: FlyBase:FBrf0238440

Axiom
annotated source: mushroom body calyx
annotated property: hasExactSynonym
annotated target: CA
database_cross_reference: FlyBase:FBrf0224194
has synonym type: BRAIN NAME ABV

Axiom
annotated source: mushroom body calyx
annotated property: hasNarrowSynonym
annotated target: main calyx
database_cross_reference: FlyBase:FBrf0205263

Kenyon cell
type: Class
subclass of: mushroom body intrinsic neuron
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: overlaps
  some values from: mushroom body pedunculus
subclass of: Restriction
  on property: develops from
  some values from: neuroblast MBp
subclass of: Restriction
  on property: receives synaptic input in region
  some values from: mushroom body calyx
definition: Intrinsic neuron of the mushroom body. They have tightly-packed cell bodies, situated in the rind above the calyx of the mushroom body (Ito et al., 1997). Four short fascicles, one per lineage, extend from the cell bodies of the Kenyon cells into the calyx (Ito et al., 1997). These 4 smaller fascicles converge in the calyx where they arborize and form pre- and post-synaptic terminals (Christiansen et al., 2011), with different Kenyon cells receiving input in different calyx regions/accessory calyces (Tanaka et al., 2008). They emerge from the calyx as a thick axon bundle referred to as the peduncle that bifurcates to innervate the dorsal and medial lobes of the mushroom body (Tanaka et al., 2008).
database_cross_reference: CL:0000673
database_cross_reference: VFB:FBbt_00003686
has exact synonym: KC
has exact synonym: intrinsic cell of mushroom body
has exact synonym: intrinsic neuron of mushroom body
has exact synonym: mature Kenyon cell
has OBO namespace: fly_anatomy.ontology
has related synonym: MB neuron
has related synonym: mushroom body neuron
id: FBbt:00003686
in subset: cur
comment: Pre-synaptic terminals were identified using two presynaptic markers (Brp and Dsyd-1) and post-synaptic terminals by labelling a subunit of the acetylcholine receptor (Dalpha7) in genetically labelled Kenyon cells (Christiansen et al., 2011).

Axiom
annotated source: Kenyon cell
annotated property: definition
annotated target: Intrinsic neuron of the mushroom body. They have tightly-packed cell bodies, situated in the rind above the calyx of the mushroom body (Ito et al., 1997). Four short fascicles, one per lineage, extend from the cell bodies of the Kenyon cells into the calyx (Ito et al., 1997). These 4 smaller fascicles converge in the calyx where they arborize and form pre- and post-synaptic terminals (Christiansen et al., 2011), with different Kenyon cells receiving input in different calyx regions/accessory calyces (Tanaka et al., 2008). They emerge from the calyx as a thick axon bundle referred to as the peduncle that bifurcates to innervate the dorsal and medial lobes of the mushroom body (Tanaka et al., 2008).
database_cross_reference: FlyBase:FBrf0092568
database_cross_reference: FlyBase:FBrf0205263
database_cross_reference: FlyBase:FBrf0214059

Axiom
annotated source: Kenyon cell
annotated property: hasExactSynonym
annotated target: KC
database_cross_reference: FlyBase:FBrf0246888

Axiom
annotated source: Kenyon cell
annotated property: hasExactSynonym
annotated target: mature Kenyon cell
database_cross_reference: FlyBase:FBrf0236359

Axiom
annotated source: Kenyon cell
annotated property: hasRelatedSynonym
annotated target: MB neuron
database_cross_reference: FlyBase:FBrf0111409

Axiom
annotated source: Kenyon cell
annotated property: hasRelatedSynonym
annotated target: mushroom body neuron
database_cross_reference: FlyBase:FBrf0111409

mushroom body pedunculus
type: Class
subclass of: synaptic neuropil domain
subclass of: mushroom body neuropil subdivision
definition: A bundle of neuron projections of Kenyon cells, dense with synapses, that extends from the calyx of the mushroom body to the base of the mushroom body lobe system (Ito et al., 1997).
database_cross_reference: VFB:FBbt_00003687
has exact synonym: PED
has exact synonym: peduncle
has exact synonym: peduncle of mushroom body
has exact synonym: peduncule
has exact synonym: peduncule of mushroom body
has exact synonym: pedunculus
has exact synonym: stalk of corpora pedunculata
has exact synonym: stalk of mushroom body
has OBO namespace: fly_anatomy.ontology
id: FBbt:00003687
in subset: BrainName
in subset: cur

Axiom
annotated source: mushroom body pedunculus
annotated property: definition
annotated target: A bundle of neuron projections of Kenyon cells, dense with synapses, that extends from the calyx of the mushroom body to the base of the mushroom body lobe system (Ito et al., 1997).
database_cross_reference: FlyBase:FBrf0092568

Axiom
annotated source: mushroom body pedunculus
annotated property: hasExactSynonym
annotated target: PED
database_cross_reference: FlyBase:FBrf0224194
has synonym type: BRAIN NAME ABV

lobe system of mushroom body
type: Class
subclass of: synaptic neuropil domain
subclass of: mushroom body neuropil subdivision
definition: The mushroom body lobe system consists of a vertical (dorsal) branch and a medial branch. In the larva, there are only two lobes (one dorsal, one medial), but remodeling during the pupal stage results in five lobes (two dorsal, three medial) in the adult (Lee et al., 1999).
database_cross_reference: VFB:FBbt_00003688
has OBO namespace: fly_anatomy.ontology
has related synonym: lobe of corpora pedunculata
has related synonym: lobe of mushroom body
id: FBbt:00003688
in subset: BrainName
in subset: cur

Axiom
annotated source: lobe system of mushroom body
annotated property: definition
annotated target: The mushroom body lobe system consists of a vertical (dorsal) branch and a medial branch. In the larva, there are only two lobes (one dorsal, one medial), but remodeling during the pupal stage results in five lobes (two dorsal, three medial) in the adult (Lee et al., 1999).
database_cross_reference: FlyBase:FBrf0105215
database_cross_reference: FlyBase:FBrf0111409
database_cross_reference: FlyBase:FBrf0144836

deutocerebrum
type: Class
equivalent class: Class
  intersection of: neuromere
  intersection of: Restriction
    on property: part of
    some values from: antennal segment
subclass of: neuromere
subclass of: Restriction
  on property: part of
  some values from: antennal segment
subclass of: Restriction
  on property: part of
  some values from: supraesophageal ganglion
definition: Neuromere of the antennal segment, located between the protocerebrum and tritocerebrum, connected to antennal nerve trunk (Urbach and Technau, 2003; Ito et al., 2014).
database_cross_reference: VFB:FBbt_00003923
has exact synonym: deuterocerebral neuromere
has exact synonym: deuterocerebrum
has exact synonym: deutocerebral neuromere
has OBO namespace: fly_anatomy.ontology
id: FBbt:00003923
in subset: cur

Axiom
annotated source: deutocerebrum
annotated property: definition
annotated target: Neuromere of the antennal segment, located between the protocerebrum and tritocerebrum, connected to antennal nerve trunk (Urbach and Technau, 2003; Ito et al., 2014).
database_cross_reference: FlyBase:FBrf0161020
database_cross_reference: FlyBase:FBrf0224194

Axiom
annotated source: deutocerebrum
annotated property: hasExactSynonym
annotated target: deuterocerebral neuromere
database_cross_reference: FlyBase:FBrf0092819

peptidergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002790
subclass of: neuron
subclass of: Restriction
  on property: capable of
  some values from: GO_0002790
definition: Any neuron (FBbt:00005106) that is capable of some peptide secretion (GO:0002790).
database_cross_reference: CL:0000110
database_cross_reference: VFB:FBbt_00004101
has OBO namespace: fly_anatomy.ontology
has related synonym: peptinergic neuron
id: FBbt:00004101
in subset: cur

Axiom
annotated source: peptidergic neuron
annotated property: definition
annotated target: Any neuron (FBbt:00005106) that is capable of some peptide secretion (GO:0002790).
database_cross_reference: FlyBase:FBrf0052426

head sensillum
type: Class
equivalent class: Class
  intersection of: sensillum
  intersection of: Restriction
    on property: part of
    some values from: head
subclass of: sensillum
subclass of: Restriction
  on property: part of
  some values from: head
definition: Any sensillum (FBbt:00007152) that is part of some head (FBbt:00000004).
database_cross_reference: UBERON:0000963
has OBO namespace: fly_anatomy.ontology
id: FBbt:00004114
in subset: cur

Axiom
annotated source: head sensillum
annotated property: definition
annotated target: Any sensillum (FBbt:00007152) that is part of some head (FBbt:00000004).
database_cross_reference: FBC:Autogenerated

ventral ectoderm anlage
type: Class
subclass of: developing embryonic structure
subclass of: anlage
subclass of: Restriction
  on property: part of
  some values from: ectoderm anlage
subclass of: Restriction
  on property: develops into
  some values from: ventral ectoderm
definition: Anlage that develops into the ventral ectoderm. It is found in the lateroventral trunk region of the embryo at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
has exact synonym: presumptive neuroectoderm
has exact synonym: ventral/neuroectoderm anlage
has OBO namespace: fly_anatomy.ontology
has related synonym: Asn/A VenEc
id: FBbt:00004204
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: ventral ectoderm anlage
annotated property: definition
annotated target: Anlage that develops into the ventral ectoderm. It is found in the lateroventral trunk region of the embryo at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
database_cross_reference: FlyBase:FBrf0244630

Axiom
annotated source: ventral ectoderm anlage
annotated property: hasExactSynonym
annotated target: presumptive neuroectoderm
database_cross_reference: FlyBase:FBrf0244630

Axiom
annotated source: ventral ectoderm anlage
annotated property: hasExactSynonym
annotated target: ventral/neuroectoderm anlage
database_cross_reference: FlyBase:FBrf0244630

Axiom
annotated source: ventral ectoderm anlage
annotated property: hasRelatedSynonym
annotated target: Asn/A VenEc
database_cross_reference: https://orcid.org/0000-0002-7073-9172

developing embryonic structure
type: Class
equivalent class: Class
  intersection of: developing material anatomical entity
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: developing material anatomical entity
subclass of: Restriction
  on property: part of
  some values from: embryo
definition: Any developing material anatomical entity of the embryo.
database_cross_reference: UBERON:0002050
has OBO namespace: fly_anatomy.ontology
id: FBbt:00004208
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: developing embryonic structure
annotated property: definition
annotated target: Any developing material anatomical entity of the embryo.
database_cross_reference: FBC:Autogenerated

late extended germ band embryo
type: Class
subclass of: extended germ band embryo
subclass of: Restriction
  on property: develops from
  some values from: early extended germ band embryo
definition: A collective term for stages 11 and 12.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00004450
in subset: cur

Axiom
annotated source: late extended germ band embryo
annotated property: definition
annotated target: A collective term for stages 11 and 12.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

organ system
type: Class
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: organism
definition: A division of the whole organism into specialized systems.
database_cross_reference: UBERON:0000467
has OBO namespace: fly_anatomy.ontology
id: FBbt:00004856
in subset: cur

Axiom
annotated source: organ system
annotated property: definition
annotated target: A division of the whole organism into specialized systems.
database_cross_reference: FBC:GG

integumentary system
type: Class
subclass of: organ system
definition: The organ system that forms the covering layer of the animal.
database_cross_reference: UBERON:0002416
has OBO namespace: fly_anatomy.ontology
id: FBbt:00004969
in subset: FB gloss
in subset: cur
in subset: expressionslim flybase ribbon

Axiom
annotated source: integumentary system
annotated property: definition
annotated target: The organ system that forms the covering layer of the animal.
database_cross_reference: FBC:GG

cuticle
type: Class
subclass of: BFO_0000002
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: integumentary system
subclass of: Restriction
  on property: develops from
  some values from: epidermis
definition: The outer non-living layer of the integumentary system that is secreted by the underlying epidermis.
database_cross_reference: UBERON:0001001
has OBO namespace: fly_anatomy.ontology
id: FBbt:00004970
in subset: FB gloss
in subset: cur

Axiom
annotated source: cuticle
annotated property: definition
annotated target: The outer non-living layer of the integumentary system that is secreted by the underlying epidermis.
database_cross_reference: FlyBase:FBrf0064790

trichome
type: Class
subclass of: cuticular specialization
definition: Non-innervated projection of the cuticle around an actin-rich cellular process of an underlying epidermal cell.
database_cross_reference: UBERON:6004979
has OBO namespace: fly_anatomy.ontology
has related synonym: cell hair
id: FBbt:00004979
in subset: cur

Axiom
annotated source: trichome
annotated property: definition
annotated target: Non-innervated projection of the cuticle around an actin-rich cellular process of an underlying epidermal cell.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

embryonic/larval cuticle
type: Class
subclass of: cuticle
subclass of: Restriction
  on property: part of
  some values from: larval integumentary system
definition: Cuticle of the late embryo or larva.
database_cross_reference: UBERON:6004983
has exact synonym: larval cuticle
has OBO namespace: fly_anatomy.ontology
id: FBbt:00004983
in subset: cur

Axiom
annotated source: embryonic/larval cuticle
annotated property: definition
annotated target: Cuticle of the late embryo or larva.
database_cross_reference: FlyBase:FBrf0234504

epidermis
type: Class
subclass of: cuboidal/columnar epithelium
subclass of: Restriction
  on property: part of
  some values from: integumentary system
definition: Tissue composed of epithelial cells. It secretes and underlies the cuticle.
database_cross_reference: UBERON:0007376
has OBO namespace: fly_anatomy.ontology
has related synonym: hypoderm
has related synonym: hypodermis
id: FBbt:00004993
in subset: FB gloss
in subset: cur

Axiom
annotated source: epidermis
annotated property: definition
annotated target: Tissue composed of epithelial cells. It secretes and underlies the cuticle.
database_cross_reference: FlyBase:FBrf0064790

digestive system
type: Class
subclass of: organ system
definition: The organ system involved in the absorption of nutrients.
database_cross_reference: UBERON:0001007
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005055
in subset: FB gloss
in subset: cur
in subset: expressionslim flybase ribbon

Axiom
annotated source: digestive system
annotated property: definition
annotated target: The organ system involved in the absorption of nutrients.
database_cross_reference: FBC:GG

apodeme
type: Class
subclass of: integumentary specialization
definition: A cuticular ingrowth of the exoskeleton, sometimes only a peg, frequently ridge-like, and often serving as a muscle attachment site. Does not generally correspond to superficial invaginations.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005091
in subset: FB gloss
in subset: cur

Axiom
annotated source: apodeme
annotated property: definition
annotated target: A cuticular ingrowth of the exoskeleton, sometimes only a peg, frequently ridge-like, and often serving as a muscle attachment site. Does not generally correspond to superficial invaginations.
database_cross_reference: FlyBase:FBrf0111704
database_cross_reference: FlyBase:FBrf0166419
database_cross_reference: FlyBase:FBrf0230923

nervous system
type: Class
subclass of: organ system
definition: All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.
database_cross_reference: UBERON:0001016
database_cross_reference: VFB:FBbt_00005093
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005093
in subset: cur
in subset: expressionslim flybase ribbon

Axiom
annotated source: nervous system
annotated property: definition
annotated target: All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.
database_cross_reference: FlyBase:FBrf0166419

central nervous system
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: Collective name for all the nerve centers and their connective in the insect's body. In the context of Drosophila refers to the part of the nervous system consisting of the brain and ventral ganglia.
database_cross_reference: UBERON:0001017
database_cross_reference: VFB:FBbt_00005094
has OBO namespace: fly_anatomy.ontology
has related synonym: CNS
id: FBbt:00005094
in subset: FB gloss
in subset: cur

Axiom
annotated source: central nervous system
annotated property: definition
annotated target: Collective name for all the nerve centers and their connective in the insect's body. In the context of Drosophila refers to the part of the nervous system consisting of the brain and ventral ganglia.
database_cross_reference: FBC:GG
database_cross_reference: FlyBase:FBrf0166419

brain
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: Anterodorsal portion of the central nervous system. The neuromeres considered to be part of the brain vary by stage. In the larva, the cerebral (supraesophageal) neuromeres, which form a bilateral pair of lobes, constitute the brain (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019). During metamorphosis, the gnathal ganglion separates from the prothoracic neuromere and fuses with the supraesophageal ganglion, to become the ventral part of the adult brain (Ito et al., 2014; Hartenstein et al., 2018; Kendroud et al., 2018).
database_cross_reference: UBERON:0000955
database_cross_reference: VFB:FBbt_00005095
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005095
in subset: FB gloss
in subset: cur

Axiom
annotated source: brain
annotated property: definition
annotated target: Anterodorsal portion of the central nervous system. The neuromeres considered to be part of the brain vary by stage. In the larva, the cerebral (supraesophageal) neuromeres, which form a bilateral pair of lobes, constitute the brain (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019). During metamorphosis, the gnathal ganglion separates from the prothoracic neuromere and fuses with the supraesophageal ganglion, to become the ventral part of the adult brain (Ito et al., 2014; Hartenstein et al., 2018; Kendroud et al., 2018).
database_cross_reference: FlyBase:FBrf0161020
database_cross_reference: FlyBase:FBrf0224194
database_cross_reference: FlyBase:FBrf0225812
database_cross_reference: FlyBase:FBrf0237251
database_cross_reference: FlyBase:FBrf0237252
database_cross_reference: FlyBase:FBrf0244240

peripheral nervous system
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: The outer parts of the nervous system that perform sensory and motor functions.
database_cross_reference: UBERON:0000010
database_cross_reference: VFB:FBbt_00005098
has OBO namespace: fly_anatomy.ontology
has related synonym: PNS
id: FBbt:00005098
in subset: FB gloss
in subset: cur

Axiom
annotated source: peripheral nervous system
annotated property: definition
annotated target: The outer parts of the nervous system that perform sensory and motor functions.
database_cross_reference: FBC:GG
database_cross_reference: FlyBase:FBrf0064796

neuron
type: Class
equivalent class: Class
  intersection of: CL_0000540
  intersection of: Restriction
    on property: part of
    some values from: Drosophila melanogaster
subclass of: CL_0000540
subclass of: somatic cell
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: Electrically active cell of the nervous system which has an axon and/or dendrite and which is synapsed with other cells and/or has other cells synapsed to it.
database_cross_reference: CL:0000540
database_cross_reference: VFB:FBbt_00005106
has OBO namespace: fly_anatomy.ontology
has related synonym: nerve cell
id: FBbt:00005106
in subset: EmbDevSlim
in subset: FB gloss
in subset: cur
in subset: larval OF
in subset: scrnaseq slim

Axiom
annotated source: neuron
annotated property: definition
annotated target: Electrically active cell of the nervous system which has an axon and/or dendrite and which is synapsed with other cells and/or has other cells synapsed to it.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

sensory neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050906
subclass of: CL_0000101
subclass of: sensory system neuron
definition: Any neuron (FBbt:00005106) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
database_cross_reference: CL:0000101
database_cross_reference: VFB:FBbt_00005124
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005124
in subset: cur
in subset: larval OF
in subset: scrnaseq slim

Axiom
annotated source: sensory neuron
annotated property: definition
annotated target: Any neuron (FBbt:00005106) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
database_cross_reference: FBC:Autogenerated

interneuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A neuron that is entirely confined to the central nervous system and is neither a sensory neuron nor a motor neuron.
database_cross_reference: CL:0000099
database_cross_reference: VFB:FBbt_00005125
has exact synonym: central neuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005125
in subset: FB gloss
in subset: cur
in subset: larval OF
in subset: scrnaseq slim

Axiom
annotated source: interneuron
annotated property: definition
annotated target: A neuron that is entirely confined to the central nervous system and is neither a sensory neuron nor a motor neuron.
database_cross_reference: FlyBase:FBrf0216671
database_cross_reference: FlyBase:FBrf0247998

Axiom
annotated source: interneuron
annotated property: hasExactSynonym
annotated target: central neuron
database_cross_reference: FlyBase:FBrf0247998

ganglion
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: Any of a number of aggregations of neurons, glial cells and their processes, and surrounded by a glial cell and connective tissue sheath (plural: ganglia).
database_cross_reference: VFB:FBbt_00005137
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005137
in subset: FB gloss
in subset: cur
in subset: larval OF

neuropil
type: Class
subclass of: multi-cell-component structure
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: Multi-cell component structure of the central nervous system consisting largely of neuron projections (tracts and synaptic neuropil domains) and associated glial cells. This corresponds to the part of the CNS that is enclosed by the cortex.
has alternative id: FBbt:00007351
database_cross_reference: UBERON:0002606
database_cross_reference: VFB:FBbt_00005139
has OBO namespace: fly_anatomy.ontology
has related synonym: neuropil
id: FBbt:00005139

Axiom
annotated source: neuropil
annotated property: definition
annotated target: Multi-cell component structure of the central nervous system consisting largely of neuron projections (tracts and synaptic neuropil domains) and associated glial cells. This corresponds to the part of the CNS that is enclosed by the cortex.
database_cross_reference: FlyBase:FBrf0224194

neuromere
type: Class
subclass of: segmental subdivision of organ system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A segmental subdivision of the nervous system.
database_cross_reference: VFB:FBbt_00005140
has OBO namespace: fly_anatomy.ontology
has related synonym: ganglion
id: FBbt:00005140
in subset: FB gloss
in subset: cur

Axiom
annotated source: neuromere
annotated property: definition
annotated target: A segmental subdivision of the nervous system.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

glial cell
type: Class
subclass of: BFO_0000002
subclass of: somatic cell
subclass of: Restriction
  on property: part of
  some values from: nervous system
subclass of: Restriction
  on property: develops from
  some values from: glioblast
definition: A supporting cell of the nervous system.
database_cross_reference: CL:0000125
database_cross_reference: VFB:FBbt_00005144
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005144
in subset: FB gloss
in subset: cur
in subset: scrnaseq slim

Axiom
annotated source: glial cell
annotated property: definition
annotated target: A supporting cell of the nervous system.
database_cross_reference: FBC:GG

glioblast
type: Class
subclass of: neuroblast
definition: Progenitor cell that gives rise only to glial cells and not neurons (Hartenstein, 2011).
database_cross_reference: CL:0000340
database_cross_reference: VFB:FBbt_00005145
has exact synonym: glial precursor cell
has OBO namespace: fly_anatomy.ontology
has related synonym: GP
id: FBbt:00005145
in subset: cur

Axiom
annotated source: glioblast
annotated property: definition
annotated target: Progenitor cell that gives rise only to glial cells and not neurons (Hartenstein, 2011).
database_cross_reference: FlyBase:FBrf0064795
database_cross_reference: FlyBase:FBrf0214261

Axiom
annotated source: glioblast
annotated property: hasRelatedSynonym
annotated target: GP
database_cross_reference: FlyBase:FBrf0055900

neuroblast
type: Class
subclass of: somatic stem cell
definition: Precursor of the central nervous system that derives from the neurogenic region of the ectoderm or the mesectoderm (Doe, 1992; Schmid et al., 1999; Crews, 2019). It produces neurons and/or glia (Doe, 1992; Beckervordersandforth et al., 2008). Neuroblasts may also divide during adult life to regenerate the adult brain (Fernandez-Hernandez et al., 2013).
database_cross_reference: CL:0000338
database_cross_reference: VFB:FBbt_00005146
has exact synonym: neural stem cell
has OBO namespace: fly_anatomy.ontology
has related synonym: NB
id: FBbt:00005146
in subset: EmbDevSlim
in subset: FB gloss
in subset: cur
comment: Adult neurogenesis demonstrated in the adult optic lobe in response to injury (Fernandez-Hernandez et al., 2013).

Axiom
annotated source: neuroblast
annotated property: definition
annotated target: Precursor of the central nervous system that derives from the neurogenic region of the ectoderm or the mesectoderm (Doe, 1992; Schmid et al., 1999; Crews, 2019). It produces neurons and/or glia (Doe, 1992; Beckervordersandforth et al., 2008). Neuroblasts may also divide during adult life to regenerate the adult brain (Fernandez-Hernandez et al., 2013).
database_cross_reference: FlyBase:FBrf0055900
database_cross_reference: FlyBase:FBrf0112030
database_cross_reference: FlyBase:FBrf0205499
database_cross_reference: FlyBase:FBrf0222020
database_cross_reference: FlyBase:FBrf0244240

Axiom
annotated source: neuroblast
annotated property: hasExactSynonym
annotated target: neural stem cell
database_cross_reference: FlyBase:FBrf0211926

sense organ
type: Class
equivalent class: Class
  intersection of: multicellular structure
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050906
subclass of: BFO_0000040
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: sensory system
subclass of: Restriction
  on property: capable of
  some values from: GO_0050906
definition: Multicellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system.
database_cross_reference: UBERON:0000020
database_cross_reference: VFB:FBbt_00005155
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005155
in subset: FB gloss
in subset: cur
in subset: hidden assertion
in subset: larval OF

Axiom
annotated source: sense organ
annotated property: definition
annotated target: Multicellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

photoreceptor
type: Class
equivalent class: Class
  intersection of: sense organ
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050962
subclass of: sense organ
subclass of: Restriction
  on property: part of
  some values from: visual system
subclass of: Restriction
  on property: capable of
  some values from: GO_0050962
definition: A light sensitive sense organ.
database_cross_reference: UBERON:0000970
database_cross_reference: VFB:FBbt_00005162
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005162
in subset: FB gloss
in subset: cur

Axiom
annotated source: photoreceptor
annotated property: definition
annotated target: A light sensitive sense organ.
database_cross_reference: FBC:GG

sensory organ cell
type: Class
equivalent class: Class
  intersection of: somatic cell
  intersection of: Restriction
    on property: overlaps
    some values from: sense organ
subclass of: somatic cell
subclass of: Restriction
  on property: overlaps
  some values from: sense organ
definition: Any somatic cell (FBbt:00100318) that overlaps some sense organ (FBbt:00005155).
has OBO namespace: fly_anatomy.ontology
has related synonym: SOC
id: FBbt:00005163
in subset: cur
in subset: scrnaseq slim

Axiom
annotated source: sensory organ cell
annotated property: definition
annotated target: Any somatic cell (FBbt:00100318) that overlaps some sense organ (FBbt:00005155).
database_cross_reference: FBC:Autogenerated

pre-blastoderm embryo
type: Class
subclass of: embryo
definition: Embryo prior to the formation of the syncitial blastoderm, shortly after nuclear cycle 9 (Foe and Alberts, 1983; Jaeger et al., 2012). This period lasts from fertilization to the end of embryonic stage 3 (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FBdv:00005290
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005290

Axiom
annotated source: pre-blastoderm embryo
annotated property: definition
annotated target: Embryo prior to the formation of the syncitial blastoderm, shortly after nuclear cycle 9 (Foe and Alberts, 1983; Jaeger et al., 2012). This period lasts from fertilization to the end of embryonic stage 3 (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0039741
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0220623

stage 1 embryo
type: Class
subclass of: cleavage stage embryo
subclass of: pre-blastoderm embryo
definition: Nuclear divisions 1 and 2. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005291
in subset: deprecated
comment: DEPRECATION WARNING.

Axiom
annotated source: stage 1 embryo
annotated property: definition
annotated target: Nuclear divisions 1 and 2. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

stage 2 embryo
type: Class
subclass of: BFO_0000002
subclass of: cleavage stage embryo
subclass of: pre-blastoderm embryo
subclass of: Restriction
  on property: develops from
  some values from: stage 1 embryo
definition: Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005293
in subset: deprecated
comment: DEPRECATION WARNING.

Axiom
annotated source: stage 2 embryo
annotated property: definition
annotated target: Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL).
database_cross_reference: FlyBase:FBrf0089570

stage 3 embryo
type: Class
subclass of: BFO_0000002
subclass of: cleavage stage embryo
subclass of: syncytial blastoderm embryo
subclass of: Restriction
  on property: develops from
  some values from: stage 2 embryo
definition: Nuclear division 9. The cleavage nuclei complete there migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005301
in subset: deprecated
comment: DEPRECATION WARNING.

Axiom
annotated source: stage 3 embryo
annotated property: definition
annotated target: Nuclear division 9. The cleavage nuclei complete there migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

blastoderm embryo
type: Class
subclass of: embryo
definition: Embryo during the blastoderm stage, where most nuclei are found at the cortex (periphery) of the embryo (Foe and Alberts, 1983; Jaeger et al., 2012). The blastoderm stage begins shortly after completion of the ninth cleavage division and lasts until the onset of gastrulation, including cleavage cycles 10-14A (Foe and Alberts, 1983; Jaeger et al., 2012). This corresponds to embryonic stages 4 (syncitial blastoderm stage) and 5 (cellular blastoderm stage) (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FBdv:00005304
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005304

Axiom
annotated source: blastoderm embryo
annotated property: definition
annotated target: Embryo during the blastoderm stage, where most nuclei are found at the cortex (periphery) of the embryo (Foe and Alberts, 1983; Jaeger et al., 2012). The blastoderm stage begins shortly after completion of the ninth cleavage division and lasts until the onset of gastrulation, including cleavage cycles 10-14A (Foe and Alberts, 1983; Jaeger et al., 2012). This corresponds to embryonic stages 4 (syncitial blastoderm stage) and 5 (cellular blastoderm stage) (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0039741
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0220623

syncytial blastoderm embryo
type: Class
subclass of: blastoderm embryo
definition: A blastoderm embryo prior to cellularization (corresponds to embryonic stages 3 and 4).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005305
in subset: cur
in subset: deprecated
comment: DEPRECATION WARNING.

Axiom
annotated source: syncytial blastoderm embryo
annotated property: definition
annotated target: A blastoderm embryo prior to cellularization (corresponds to embryonic stages 3 and 4).
database_cross_reference: FBC:GG
database_cross_reference: https://orcid.org/0000-0002-7073-9172

stage 4 embryo
type: Class
subclass of: BFO_0000002
subclass of: cleavage stage embryo
subclass of: syncytial blastoderm embryo
subclass of: Restriction
  on property: develops from
  some values from: stage 3 embryo
definition: Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005306
in subset: deprecated
comment: DEPRECATION WARNING.

Axiom
annotated source: stage 4 embryo
annotated property: definition
annotated target: Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

stage 5 embryo
type: Class
subclass of: BFO_0000002
subclass of: blastoderm embryo
subclass of: Restriction
  on property: develops from
  some values from: stage 4 embryo
definition: Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees C: approximately 40 minutes (130-170 minutes after egg laying).
has OBO namespace: fly_anatomy.ontology
has related synonym: cellular blastoderm embryo
id: FBbt:00005311
in subset: deprecated
comment: DEPRECATION WARNING.

Axiom
annotated source: stage 5 embryo
annotated property: definition
annotated target: Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees C: approximately 40 minutes (130-170 minutes after egg laying).
database_cross_reference: FBC:MA
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: https://orcid.org/0000-0002-7073-9172

gastrula embryo
type: Class
subclass of: BFO_0000002
subclass of: embryo
subclass of: Restriction
  on property: develops from
  some values from: blastoderm embryo
definition: Embryo that is in the process of gastrulation (encompassing embryonic stages 6-8), during which complex morphogenetic movements result in the formation of the three germ layers; ectoderm, mesoderm and endoderm (Hartenstein, 1993).
database_cross_reference: FBdv:00005317
database_cross_reference: UBERON:0004734
has exact synonym: gastrulation stage embryo
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005317

Axiom
annotated source: gastrula embryo
annotated property: definition
annotated target: Embryo that is in the process of gastrulation (encompassing embryonic stages 6-8), during which complex morphogenetic movements result in the formation of the three germ layers; ectoderm, mesoderm and endoderm (Hartenstein, 1993).
database_cross_reference: FlyBase:FBrf0064803

extended germ band embryo
type: Class
subclass of: BFO_0000002
subclass of: embryo
subclass of: Restriction
  on property: develops from
  some values from: gastrula embryo
definition: Embryo during stages 9-12.
database_cross_reference: FBdv:00005321
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005321

Axiom
annotated source: extended germ band embryo
annotated property: definition
annotated target: Embryo during stages 9-12.
database_cross_reference: FlyBase:FBrf0229323
database_cross_reference: https://orcid.org/0000-0002-7073-9172

dorsal closure embryo
type: Class
subclass of: BFO_0000002
subclass of: embryo
subclass of: Restriction
  on property: develops from
  some values from: late extended germ band embryo
definition: Embryo during the dorsal closure stage, which corresponds to stages 13-15 (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997). Dorsal closure occurs by extension of the dorsal epidermal primordium on either side, leading to fusion at the dorsal midline (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FBdv:00005331
has OBO namespace: fly_anatomy.ontology
has related synonym: contracted germ band embryo
has related synonym: head involution embryo
id: FBbt:00005331

Axiom
annotated source: dorsal closure embryo
annotated property: definition
annotated target: Embryo during the dorsal closure stage, which corresponds to stages 13-15 (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997). Dorsal closure occurs by extension of the dorsal epidermal primordium on either side, leading to fusion at the dorsal midline (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0064803
database_cross_reference: FlyBase:FBrf0089570

late embryo
type: Class
subclass of: BFO_0000002
subclass of: embryo
subclass of: Restriction
  on property: develops from
  some values from: dorsal closure embryo
definition: Embryo during stages 16 and 17.
database_cross_reference: FBdv:00005333
database_cross_reference: UBERON:0000323
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005333

Axiom
annotated source: late embryo
annotated property: definition
annotated target: Embryo during stages 16 and 17.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

hindgut
type: Class
subclass of: BFO_0000002
subclass of: multi-tissue structure
subclass of: gut section
subclass of: Restriction
  on property: expresses
  some values from: FBgn0011723
definition: A posterior part of the alimentary canal derived from the ectoderm. It extends anteriorly from close to the point of attachment of the Malpighian tubules to the anus. It is lined on its luminal side by an impermeable cuticle (Skaer, 1993).
database_cross_reference: UBERON:0001046
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005384
in subset: FB gloss
in subset: cur
comment: Adult and larval hindguts express the transcription factor brachyenteron (Sawyer et al., 2017).

Axiom
annotated source: hindgut
annotated property: definition
annotated target: A posterior part of the alimentary canal derived from the ectoderm. It extends anteriorly from close to the point of attachment of the Malpighian tubules to the anus. It is lined on its luminal side by an impermeable cuticle (Skaer, 1993).
database_cross_reference: FBC:GG
database_cross_reference: FlyBase:FBrf0064792

presumptive embryonic/larval integumentary system
type: Class
subclass of: presumptive embryonic/larval system
definition: The sum of all the structures in the embryo that will develop into the embryonic/larval integumentary system.
has OBO namespace: fly_anatomy.ontology
has related synonym: embryonic integumentary system
id: FBbt:00005392
in subset: cur
in subset: expressionslim flybase ribbon

Axiom
annotated source: presumptive embryonic/larval integumentary system
annotated property: definition
annotated target: The sum of all the structures in the embryo that will develop into the embryonic/larval integumentary system.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: presumptive embryonic/larval integumentary system
annotated property: hasRelatedSynonym
annotated target: embryonic integumentary system
database_cross_reference: https://orcid.org/0000-0002-7073-9172

larval integumentary system
type: Class
equivalent class: Class
  intersection of: integumentary system
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: integumentary system
subclass of: Restriction
  on property: part of
  some values from: larva
definition: Integumentary system of the late embryo or larva.
database_cross_reference: UBERON:6005393
has exact synonym: embryonic/larval integumentary system
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005393
in subset: cur

Axiom
annotated source: larval integumentary system
annotated property: definition
annotated target: Integumentary system of the late embryo or larva.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

embryonic epidermis
type: Class
subclass of: epidermis
subclass of: Restriction
  on property: part of
  some values from: presumptive embryonic/larval integumentary system
definition: Epidermis of the embryo.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005397
in subset: cur

Axiom
annotated source: embryonic epidermis
annotated property: definition
annotated target: Epidermis of the embryo.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

mushroom body vertical lobe
type: Class
subclass of: synaptic neuropil domain
subclass of: mushroom body neuropil subdivision
subclass of: Restriction
  on property: part of
  some values from: lobe system of mushroom body
definition: Bundle of Kenyon cell projections that arises from the anterior end of the pedunculus and projects dorsally. It consists of two components: the alpha lobe and alpha' lobe.
database_cross_reference: VFB:FBbt_00005407
has exact synonym: VL
has exact synonym: dorsal lobe of mushroom body
has exact synonym: vertical branch of mushroom body
has exact synonym: vertical lobe of mushroom body
has OBO namespace: fly_anatomy.ontology
has related synonym: dorsal lobe
id: FBbt:00005407
in subset: cur

Axiom
annotated source: mushroom body vertical lobe
annotated property: definition
annotated target: Bundle of Kenyon cell projections that arises from the anterior end of the pedunculus and projects dorsally. It consists of two components: the alpha lobe and alpha' lobe.
database_cross_reference: FlyBase:FBrf0224194
database_cross_reference: VFB_vol:00005407

Axiom
annotated source: mushroom body vertical lobe
annotated property: hasExactSynonym
annotated target: VL
database_cross_reference: FlyBase:FBrf0224194
has synonym type: BRAIN NAME ABV

mushroom body medial lobe
type: Class
subclass of: synaptic neuropil domain
subclass of: mushroom body neuropil subdivision
subclass of: Restriction
  on property: part of
  some values from: lobe system of mushroom body
definition: A bundle of Kenyon cell projections that arises from the anterior end of the pedunculus and projects medially. It consists of three components: the beta lobe, beta' lobe and gamma lobe.
has alternative id: FBbt:00003692
database_cross_reference: VFB:FBbt_00005408
has exact synonym: ML
has exact synonym: horizontal lobe of mushroom body
has exact synonym: medial branch of mushroom body
has exact synonym: medial lobe of mushroom body
has OBO namespace: fly_anatomy.ontology
has related synonym: medial lobe
id: FBbt:00005408
in subset: BrainName
in subset: cur

Axiom
annotated source: mushroom body medial lobe
annotated property: definition
annotated target: A bundle of Kenyon cell projections that arises from the anterior end of the pedunculus and projects medially. It consists of three components: the beta lobe, beta' lobe and gamma lobe.
database_cross_reference: FlyBase:FBrf0224194
database_cross_reference: VFB_vol:00005408

Axiom
annotated source: mushroom body medial lobe
annotated property: hasExactSynonym
annotated target: ML
database_cross_reference: FlyBase:FBrf0224194
has synonym type: BRAIN NAME ABV

anlage in statu nascendi
type: Class
subclass of: developing embryonic structure
definition: Domain that is in the process of forming an anlage and does not yet coincide 1:1 with a mature structure. These domains can be identified based on the expression of genes characteristic of the corresponding anlagen and are typically found in the early blastoderm.
has OBO namespace: fly_anatomy.ontology
has related synonym: A0
id: FBbt:00005413
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: anlage in statu nascendi
annotated property: definition
annotated target: Domain that is in the process of forming an anlage and does not yet coincide 1:1 with a mature structure. These domains can be identified based on the expression of genes characteristic of the corresponding anlagen and are typically found in the early blastoderm.
database_cross_reference: FlyBase:FBrf0155831
database_cross_reference: FlyBase:FBrf0178740

central brain anlage in statu nascendi
type: Class
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: stage 5 embryo
subclass of: Restriction
  on property: part of
  some values from: anterior ectoderm anlage
definition: Anlage in statu nascendi of the embryonic central brain in a stage 5 embryo. It will give rise to the central brain anlage.
has exact synonym: Asn CenBr
has OBO namespace: fly_anatomy.ontology
has related synonym: A0ProcEC
has related synonym: procephalic ectoderm anlage in statu nascendi
id: FBbt:00005415
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: central brain anlage in statu nascendi
annotated property: definition
annotated target: Anlage in statu nascendi of the embryonic central brain in a stage 5 embryo. It will give rise to the central brain anlage.
database_cross_reference: FBC:VH

Axiom
annotated source: central brain anlage in statu nascendi
annotated property: hasExactSynonym
annotated target: Asn CenBr
database_cross_reference: https://orcid.org/0000-0002-7073-9172

visual anlage in statu nascendi
type: Class
subclass of: anlage in statu nascendi
subclass of: Restriction
  on property: part of
  some values from: stage 5 embryo
subclass of: Restriction
  on property: part of
  some values from: anterior ectoderm anlage
definition: Anlage in statu nascendi of the visual system in a stage 5 embryo that will give rise to the visual system anlage.
has exact synonym: Asn VisSys
has OBO namespace: fly_anatomy.ontology
has related synonym: A0Vis
id: FBbt:00005425
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: visual anlage in statu nascendi
annotated property: definition
annotated target: Anlage in statu nascendi of the visual system in a stage 5 embryo that will give rise to the visual system anlage.
database_cross_reference: FBC:VH

Axiom
annotated source: visual anlage in statu nascendi
annotated property: hasExactSynonym
annotated target: Asn VisSys
database_cross_reference: https://orcid.org/0000-0002-7073-9172

anlage
type: Class
subclass of: portion of tissue
subclass of: developing material anatomical entity
definition: Population of contiguous cells, typically arranged in one plane, that is morphologically indistinct from surrounding cells, but already corresponds to a later organ/tissue and can be identified based on gene expression or lineage tracing (Tomancak et al., 2002; Hartenstein, 2004).
database_cross_reference: UBERON:0007688
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005426
in subset: EmbDevSlim
in subset: FB gloss
in subset: cur
in subset: expressionslim flybase ribbon

Axiom
annotated source: anlage
annotated property: definition
annotated target: Population of contiguous cells, typically arranged in one plane, that is morphologically indistinct from surrounding cells, but already corresponds to a later organ/tissue and can be identified based on gene expression or lineage tracing (Tomancak et al., 2002; Hartenstein, 2004).
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0155831
database_cross_reference: FlyBase:FBrf0178740

ectoderm anlage
type: Class
subclass of: developing embryonic structure
subclass of: anlage
subclass of: Restriction
  on property: develops into
  some values from: ectoderm
definition: Cells of the early embryo that will become the ectoderm following gastrulation (Campos-Ortega and Hartenstein, 1997). It remains at the surface of the embryo as the endodermal and mesodermal anlagen invaginate (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: UBERON:6005427
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005427
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: ectoderm anlage
annotated property: definition
annotated target: Cells of the early embryo that will become the ectoderm following gastrulation (Campos-Ortega and Hartenstein, 1997). It remains at the surface of the embryo as the endodermal and mesodermal anlagen invaginate (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0155831
database_cross_reference: FlyBase:FBrf0244630

visual anlage
type: Class
subclass of: BFO_0000002
subclass of: developing embryonic structure
subclass of: anlage
subclass of: Restriction
  on property: part of
  some values from: anterior ectoderm
subclass of: Restriction
  on property: part of
  some values from: gastrula embryo
subclass of: Restriction
  on property: develops from
  some values from: visual anlage in statu nascendi
subclass of: Restriction
  on property: develops into
  some values from: visual primordium
definition: Anlage of the visual system in the gastrula embryo that will give rise to the visual primordium.
has exact synonym: A VisSys
has OBO namespace: fly_anatomy.ontology
has related synonym: AVis
id: FBbt:00005434
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: visual anlage
annotated property: definition
annotated target: Anlage of the visual system in the gastrula embryo that will give rise to the visual primordium.
database_cross_reference: FBC:VH

Axiom
annotated source: visual anlage
annotated property: hasExactSynonym
annotated target: A VisSys
database_cross_reference: https://orcid.org/0000-0002-7073-9172

primordium
type: Class
subclass of: BFO_0000002
subclass of: developing material anatomical entity
subclass of: Restriction
  on property: develops from
  some values from: anlage
definition: Precursor structure that can be recognized based on its distinct morphology and will give rise to one or more differentiated structures (Tomancak et al., 2002; Hartenstein, 2004). It develops from an anlage and may contain smaller anlage and primordia that will produce substructures (Tomancak et al., 2002).
database_cross_reference: UBERON:0001048
has OBO namespace: fly_anatomy.ontology
has related synonym: P
has related synonym: placode
id: FBbt:00005495
in subset: EmbDevSlim
in subset: FB gloss
in subset: cur
in subset: expressionslim flybase ribbon

Axiom
annotated source: primordium
annotated property: definition
annotated target: Precursor structure that can be recognized based on its distinct morphology and will give rise to one or more differentiated structures (Tomancak et al., 2002; Hartenstein, 2004). It develops from an anlage and may contain smaller anlage and primordia that will produce substructures (Tomancak et al., 2002).
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0155831
database_cross_reference: FlyBase:FBrf0178740

mushroom body primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: central brain primordium
subclass of: Restriction
  on property: part of
  some values from: embryonic central brain
subclass of: Restriction
  on property: develops into
  some values from: mushroom body
definition: Embryonic structure from which the mushroom body is derived. The development of the mushroom body proceeds as follows: axonogenesis of embryonic Kenyon cells starts late in embryonic stage 14. The axons from these cells extend towards the lateral protocerebral tract (LTP). During stage 16, a second set of Kenyon cell fibers form a second tract, closely apposed to the first. By late stage 16, both tracts extend anteriorly beyond the LTP to form the distal part of the peduncle. These tracts make a sharp medial turn close to the boundary with the deutocerebrum to form the medial lobe. By late stage 17 the vertical lobe has emerged as a collateral outgrowth from the point where these tracts bend. Finally, the calyx forms near to the end of embryogenesis.
has alternative id: FBbt:00005666
database_cross_reference: VFB:FBbt_00005508
has exact synonym: embryonic central brain mushroom body
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005508
in subset: cur

Axiom
annotated source: mushroom body primordium
annotated property: definition
annotated target: Embryonic structure from which the mushroom body is derived. The development of the mushroom body proceeds as follows: axonogenesis of embryonic Kenyon cells starts late in embryonic stage 14. The axons from these cells extend towards the lateral protocerebral tract (LTP). During stage 16, a second set of Kenyon cell fibers form a second tract, closely apposed to the first. By late stage 16, both tracts extend anteriorly beyond the LTP to form the distal part of the peduncle. These tracts make a sharp medial turn close to the boundary with the deutocerebrum to form the medial lobe. By late stage 17 the vertical lobe has emerged as a collateral outgrowth from the point where these tracts bend. Finally, the calyx forms near to the end of embryogenesis.
database_cross_reference: FlyBase:FBrf0144836

early embryonic primordium of adult eye
type: Class
subclass of: embryonic primordium of adult eye
subclass of: Restriction
  on property: part of
  some values from: late extended germ band embryo
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops into
  some values from: late embryonic primordium of adult eye
definition: Early primordium of the late extended germ band and dorsal closure embryo that will give rise to the adult eye. It develops from the visual primordium.
has exact synonym: adult eye primordium early
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005515
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: early embryonic primordium of adult eye
annotated property: definition
annotated target: Early primordium of the late extended germ band and dorsal closure embryo that will give rise to the adult eye. It develops from the visual primordium.
database_cross_reference: FBC:VH
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0151275
database_cross_reference: https://orcid.org/0000-0002-7073-9172

ventral epidermis primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: ventral ectoderm derivative
subclass of: Class
  intersection of: Restriction
    on property: develops into
    some values from: imaginal disc primordium
  intersection of: Restriction
    on property: develops into
    some values from: embryonic ventral epidermis
  intersection of: Restriction
    on property: develops into
    some values from: ventral trunk epidermis primordium
  intersection of: Restriction
    on property: develops into
    some values from: anal pad primordium
  intersection of: Restriction
    on property: develops into
    some values from: ventral apodeme anlage
  intersection of: Restriction
    on property: develops into
    some values from: denticle field anlage
subclass of: Restriction
  on property: part of
  some values from: early extended germ band embryo
subclass of: Restriction
  on property: develops from
  some values from: ventral neurectoderm
definition: A(n) primordium that develops into some denticle field anlage and some anal pad primordium and some embryonic ventral epidermis and some imaginal disc primordium and some ventral apodeme anlage and some ventral trunk epidermis primordium. It develops from some ventral neurectoderm.
database_cross_reference: UBERON:6005533
has OBO namespace: fly_anatomy.ontology
has related synonym: P2 iVenEp
has related synonym: venEpiP2
id: FBbt:00005533
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: ventral epidermis primordium
annotated property: definition
annotated target: A(n) primordium that develops into some denticle field anlage and some anal pad primordium and some embryonic ventral epidermis and some imaginal disc primordium and some ventral apodeme anlage and some ventral trunk epidermis primordium. It develops from some ventral neurectoderm.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: ventral epidermis primordium
annotated property: hasRelatedSynonym
annotated target: P2 iVenEp
database_cross_reference: https://orcid.org/0000-0002-7073-9172

central brain primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: extended germ band embryo
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: central brain anlage
subclass of: Restriction
  on property: develops into
  some values from: embryonic central brain
definition: Primordium of the embryonic central brain in the extended germ band and dorsal closure embryo.
has narrow synonym: P1 Cen Br
has narrow synonym: P3 CenBr
has OBO namespace: fly_anatomy.ontology
has related synonym: ProcEcP2
has related synonym: procephalic ectoderm primordium
id: FBbt:00005542
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: central brain primordium
annotated property: definition
annotated target: Primordium of the embryonic central brain in the extended germ band and dorsal closure embryo.
database_cross_reference: FBC:VH
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: central brain primordium
annotated property: hasNarrowSynonym
annotated target: P1 Cen Br
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: central brain primordium
annotated property: hasNarrowSynonym
annotated target: P3 CenBr
database_cross_reference: https://orcid.org/0000-0002-7073-9172

head epidermis primordium
type: Class
subclass of: primordium
definition: Primordium that develops into a region of head epidermis.
has OBO namespace: fly_anatomy.ontology
has related synonym: HeadEpiP3
id: FBbt:00005547
in subset: cur

ventral ectoderm
type: Class
subclass of: BFO_0000002
subclass of: developing embryonic structure
subclass of: Restriction
  on property: part of
  some values from: trunk ectoderm
subclass of: Restriction
  on property: develops from
  some values from: ventral ectoderm anlage
definition: Ventral region of the trunk ectoderm, which gives rise to the ventral epidermis and the central nervous system (Stathopoulos and Newcomb, 2020).
database_cross_reference: UBERON:6005558
has exact synonym: neuroectoderm
has exact synonym: neurogenic ectoderm
has OBO namespace: fly_anatomy.ontology
has related synonym: P2 VenEc
has related synonym: venEc
id: FBbt:00005558
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: ventral ectoderm
annotated property: definition
annotated target: Ventral region of the trunk ectoderm, which gives rise to the ventral epidermis and the central nervous system (Stathopoulos and Newcomb, 2020).
database_cross_reference: FlyBase:FBrf0244630
database_cross_reference: FlyBase:FBrf0246683

Axiom
annotated source: ventral ectoderm
annotated property: hasExactSynonym
annotated target: neuroectoderm
database_cross_reference: FlyBase:FBrf0244630

Axiom
annotated source: ventral ectoderm
annotated property: hasExactSynonym
annotated target: neurogenic ectoderm
database_cross_reference: FlyBase:FBrf0246683

Axiom
annotated source: ventral ectoderm
annotated property: hasRelatedSynonym
annotated target: P2 VenEc
database_cross_reference: https://orcid.org/0000-0002-7073-9172

embryonic central brain
type: Class
subclass of: anterior ectoderm derivative
subclass of: central brain
subclass of: Restriction
  on property: part of
  some values from: embryonic brain
subclass of: Restriction
  on property: develops from
  some values from: central brain primordium
definition: Brain of the embryo that excludes the optic lobes. It includes the protocerebrum, deutocerebrum and tritocerebrum.
database_cross_reference: VFB:FBbt_00005662
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005662
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic central brain
annotated property: definition
annotated target: Brain of the embryo that excludes the optic lobes. It includes the protocerebrum, deutocerebrum and tritocerebrum.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

embryonic central brain glial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: part of
    some values from: embryonic central brain
subclass of: CNS glial cell
subclass of: embryonic glial cell
subclass of: Restriction
  on property: part of
  some values from: embryonic central brain
definition: Glial cell of the embryonic central brain.
database_cross_reference: VFB:FBbt_00005663
has exact synonym: embryonic central brain glia
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005663
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic central brain glial cell
annotated property: definition
annotated target: Glial cell of the embryonic central brain.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

embryonic central brain neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: has soma location
    some values from: embryonic central brain
subclass of: supraesophageal ganglion neuron
subclass of: Restriction
  on property: has soma location
  some values from: embryonic central brain
definition: Neuron of the embryonic central brain.
database_cross_reference: VFB:FBbt_00005665
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005665
in subset: cur

Axiom
annotated source: embryonic central brain neuron
annotated property: definition
annotated target: Neuron of the embryonic central brain.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

embryonic head epidermis
type: Class
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: embryonic epidermis
definition: Epidermis of the embryonic head.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005741
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic head epidermis
annotated property: definition
annotated target: Epidermis of the embryonic head.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

embryonic dorsal pouch
type: Class
subclass of: dorsal pouch
subclass of: Restriction
  on property: part of
  some values from: embryonic head epidermis
definition: Epidermal pouch in the embryonic head that incorporates the acron and dorsal regions of the head segments. It forms following the movement of the dorsal fold over the clypeolabrum and procephalic lobe.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005743
in subset: EmbDevSlim
in subset: cur
comment: Note - possible redundancy between primordium term and embryonic term. ds060616.

Axiom
annotated source: embryonic dorsal pouch
annotated property: definition
annotated target: Epidermal pouch in the embryonic head that incorporates the acron and dorsal regions of the head segments. It forms following the movement of the dorsal fold over the clypeolabrum and procephalic lobe.
database_cross_reference: FlyBase:FBrf0041814

embryonic ventral epidermis
type: Class
subclass of: ventral ectoderm derivative
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: embryonic epidermis
subclass of: Restriction
  on property: develops from
  some values from: ventral epidermis primordium
definition: Epidermis of the ventral region of the embryo.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005747
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic ventral epidermis
annotated property: definition
annotated target: Epidermis of the ventral region of the embryo.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

embryonic anal pad
type: Class
subclass of: anal pad
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: embryonic ventral epidermis
subclass of: Restriction
  on property: develops from
  some values from: anal pad primordium
definition: Anal pad of the embryo.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005748
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic anal pad
annotated property: definition
annotated target: Anal pad of the embryo.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

embryonic ventral apodeme
type: Class
subclass of: apodeme
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: embryonic ventral epidermis
subclass of: Restriction
  on property: develops from
  some values from: ventral apodeme primordium
definition: Ventral halve of an embryonic apodeme. The discontinuity between dorsal and ventral halves is visible on a lateral view.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005749
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic ventral apodeme
annotated property: definition
annotated target: Ventral halve of an embryonic apodeme. The discontinuity between dorsal and ventral halves is visible on a lateral view.
database_cross_reference: FlyBase:FBrf0089570

anal pad
type: Class
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: hindgut
definition: Plate or plates that surrounds the anus.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005785
in subset: cur

Axiom
annotated source: anal pad
annotated property: definition
annotated target: Plate or plates that surrounds the anus.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

mushroom body
type: Class
subclass of: BFO_0000040
subclass of: anterior ectoderm derivative
subclass of: synaptic neuropil block
subclass of: Restriction
  on property: part of
  some values from: protocerebrum
subclass of: Restriction
  on property: develops from
  some values from: mushroom body primordium
subclass of: Restriction
  on property: capable of part of
  some values from: GO_0007613
definition: Bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. The mushroom body is divided into: the calyx, which is closest to the cortex and receives sensory interneuron afferents; the pedunculus, which is a thick axon bundle extending from the calyx to the base of the lobes; and the mushroom body lobe system, which consists of a vertical branch and a medial branch, which have different structures at different life stages (Lee et al., 1999; Ito et al., 2014).
database_cross_reference: UBERON:0001058
database_cross_reference: VFB:FBbt_00005801
has exact synonym: MB
has exact synonym: corpora pedunculata
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005801
in subset: BrainName
in subset: FB gloss
in subset: cur
comment: This term as defined in Ito et al. (2014) corresponds to both the mushroom body (MB) and calyx (Cal) of Chiang et al. (2011).

Axiom
annotated source: mushroom body
annotated property: definition
annotated target: Bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. The mushroom body is divided into: the calyx, which is closest to the cortex and receives sensory interneuron afferents; the pedunculus, which is a thick axon bundle extending from the calyx to the base of the lobes; and the mushroom body lobe system, which consists of a vertical branch and a medial branch, which have different structures at different life stages (Lee et al., 1999; Ito et al., 2014).
database_cross_reference: FlyBase:FBrf0111409
database_cross_reference: FlyBase:FBrf0224194
database_cross_reference: FlyBase:FBrf0248215

Axiom
annotated source: mushroom body
annotated property: hasExactSynonym
annotated target: MB
database_cross_reference: FlyBase:FBrf0219809

Bolwig organ
type: Class
subclass of: larval ocular segment sense organ
subclass of: photoreceptor
subclass of: internal sensillum
subclass of: embryonic/larval head sensillum
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: late embryo
subclass of: Restriction
  on property: develops from
  some values from: Bolwig organ primordium
subclass of: Restriction
  on property: capable of
  some values from: GO_0050908
definition: Visual organ of the larva. It consists of a dense cluster of 12 ciliated photoreceptor neurons located on either side of the midline in a dorsomedial position in the anterior region of the larva.
has alternative id: FBbt:00002643
has alternative id: FBbt:00005742
has alternative id: FBbt:00015250
database_cross_reference: UBERON:6005805
database_cross_reference: VFB:FBbt_00005805
has exact synonym: Bolwig's organ
has exact synonym: embryonic Bolwig's organ
has exact synonym: embryonic visual system
has exact synonym: larval Bolwig's organ
has exact synonym: larval eye
has exact synonym: stemmata organ
has OBO namespace: fly_anatomy.ontology
has related synonym: dorsocaudal pharyngeal sense organ
id: FBbt:00005805
in subset: FB gloss
in subset: cur
comment: Location in ocular segment on basis of FBrf0075072.

Axiom
annotated source: Bolwig organ
annotated property: definition
annotated target: Visual organ of the larva. It consists of a dense cluster of 12 ciliated photoreceptor neurons located on either side of the midline in a dorsomedial position in the anterior region of the larva.
database_cross_reference: FlyBase:FBrf0089570

Axiom
annotated source: Bolwig organ
annotated property: hasExactSynonym
annotated target: larval eye
database_cross_reference: FlyBase:FBrf0213587

Axiom
annotated source: Bolwig organ
annotated property: hasExactSynonym
annotated target: stemmata organ
database_cross_reference: FlyBase:FBrf0047902

antennal sense organ
type: Class
equivalent class: Class
  intersection of: sense organ
  intersection of: Restriction
    on property: part of
    some values from: antennal segment
subclass of: sense organ
subclass of: Restriction
  on property: part of
  some values from: antennal segment
definition: Any sense organ (FBbt:00005155) that is part of some antennal segment (FBbt:00000009).
has alternative id: FBbt:00004171
database_cross_reference: VFB:FBbt_00005806
has exact synonym: antennal sensillum
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005806
in subset: cur

Axiom
annotated source: antennal sense organ
annotated property: definition
annotated target: Any sense organ (FBbt:00005155) that is part of some antennal segment (FBbt:00000009).
database_cross_reference: FBC:Autogenerated

dorsal pouch
type: Class
subclass of: epidermis
definition: Epidermal pouch in the head of the embryo or larva.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005807
in subset: cur

Axiom
annotated source: dorsal pouch
annotated property: definition
annotated target: Epidermal pouch in the head of the embryo or larva.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

Bolwig organ primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: late extended germ band embryo
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: visual primordium
subclass of: Restriction
  on property: develops into
  some values from: Bolwig organ
definition: Primordium of the late extended and dorsal closure embryo that gives rise to the larval Bolwig organ. It corresponds to the most posterior region that develops from the visual primordium.
database_cross_reference: UBERON:6005830
has exact synonym: Bolwig's organ primordium
has exact synonym: P1 BolOrg
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005830
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: Bolwig organ primordium
annotated property: definition
annotated target: Primordium of the late extended and dorsal closure embryo that gives rise to the larval Bolwig organ. It corresponds to the most posterior region that develops from the visual primordium.
database_cross_reference: FBC:VH
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0151275
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: Bolwig organ primordium
annotated property: hasExactSynonym
annotated target: P1 BolOrg
database_cross_reference: https://orcid.org/0000-0002-7073-9172

larval peripheral nervous system
type: Class
equivalent class: Class
  intersection of: peripheral nervous system
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: larval nervous system
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Peripheral nervous system of the embryo or larva.
database_cross_reference: VFB:FBbt_00005893
has exact synonym: embryonic/larval PNS
has exact synonym: embryonic/larval peripheral nervous system
has exact synonym: larval PNS
has OBO namespace: fly_anatomy.ontology
id: FBbt:00005893
in subset: cur
in subset: larval OF

Axiom
annotated source: larval peripheral nervous system
annotated property: definition
annotated target: Peripheral nervous system of the embryo or larva.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.
database_cross_reference: CARO:0000003
database_cross_reference: UBERON:0000061
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007001
in subset: cur
in subset: larval OF

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.
database_cross_reference: https://orcid.org/0000-0001-9114-8737
database_cross_reference: https://orcid.org/0000-0002-7073-9172

cell
type: Class
subclass of: anatomical structure
definition: Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
database_cross_reference: CARO:0000013
database_cross_reference: CL:0000000
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007002
in subset: FB gloss
in subset: cur
in subset: larval OF

Axiom
annotated source: cell
annotated property: definition
annotated target: Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
database_cross_reference: https://orcid.org/0000-0001-9114-8737

portion of tissue
type: Class
subclass of: multicellular structure
definition: Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
database_cross_reference: CARO:0000043
database_cross_reference: UBERON:0000479
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007003
in subset: cur

Axiom
annotated source: portion of tissue
annotated property: definition
annotated target: Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
database_cross_reference: https://orcid.org/0000-0001-9114-8737

epithelium
type: Class
subclass of: portion of tissue
definition: Portion of tissue, that consists of one or more layers of cells with distinct apical-basal polarity, connected to each other by cell junctions.
database_cross_reference: UBERON:0000483
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007005
in subset: cur

Axiom
annotated source: epithelium
annotated property: definition
annotated target: Portion of tissue, that consists of one or more layers of cells with distinct apical-basal polarity, connected to each other by cell junctions.
database_cross_reference: https://orcid.org/0000-0001-9114-8737

developing material anatomical entity
type: Class
subclass of: material anatomical entity
database_cross_reference: CARO:0000066
database_cross_reference: UBERON:0005423
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007006
in subset: cur

somatic precursor cell
type: Class
subclass of: developing material anatomical entity
subclass of: somatic cell
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007008
in subset: cur
in subset: scrnaseq slim

organism subdivision
type: Class
subclass of: multicellular structure
definition: Anatomical structure that is a primary subdivision of whole organism. The mereological sum of these is the whole organism.
database_cross_reference: CARO:0000032
database_cross_reference: UBERON:0000475
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007009
in subset: cur
in subset: larval OF

Axiom
annotated source: organism subdivision
annotated property: definition
annotated target: Anatomical structure that is a primary subdivision of whole organism. The mereological sum of these is the whole organism.
database_cross_reference: https://orcid.org/0000-0001-9114-8737

multi-tissue structure
type: Class
subclass of: multicellular structure
definition: 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.
database_cross_reference: CARO:0000055
database_cross_reference: UBERON:0000481
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007010
in subset: cur
in subset: larval OF

Axiom
annotated source: multi-tissue structure
annotated property: definition
annotated target: 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.
database_cross_reference: https://orcid.org/0000-0001-9114-8737

acellular anatomical structure
type: Class
subclass of: anatomical structure
database_cross_reference: CARO:0000040
database_cross_reference: UBERON:0000476
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007013
in subset: cur

stem cell
type: Class
subclass of: cell
definition: Undifferentiated cell which retains its identity while budding off cells which differentiate.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007014
in subset: cur
in subset: expressionslim flybase ribbon

Axiom
annotated source: stem cell
annotated property: definition
annotated target: Undifferentiated cell which retains its identity while budding off cells which differentiate.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

material anatomical entity
type: Class
subclass of: anatomical entity
database_cross_reference: CARO:0000006
database_cross_reference: UBERON:0000465
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007016
in subset: cur
in subset: larval OF

cuboidal/columnar epithelium
type: Class
subclass of: epithelium
definition: An epithelium consisting of columnar shaped cells.
database_cross_reference: UBERON:0000485
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007027
in subset: cur

Axiom
annotated source: cuboidal/columnar epithelium
annotated property: definition
annotated target: An epithelium consisting of columnar shaped cells.
database_cross_reference: FlyBase:FBrf0239342

trunk ectoderm
type: Class
subclass of: developing embryonic structure
subclass of: Restriction
  on property: part of
  some values from: ectoderm
definition: The region of the ectoderm posterior to the cephalic furrow.
database_cross_reference: UBERON:6007045
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007045

Axiom
annotated source: trunk ectoderm
annotated property: definition
annotated target: The region of the ectoderm posterior to the cephalic furrow.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

procephalic glioblast
type: Class
equivalent class: Class
  intersection of: glioblast
  intersection of: Restriction
    on property: part of
    some values from: central brain primordium
subclass of: embryonic glioblast
subclass of: Restriction
  on property: part of
  some values from: central brain primordium
definition: Any glioblast (FBbt:00005145) that is part of some central brain primordium (FBbt:00005542).
database_cross_reference: VFB:FBbt_00007051
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007051

Axiom
annotated source: procephalic glioblast
annotated property: definition
annotated target: Any glioblast (FBbt:00005145) that is part of some central brain primordium (FBbt:00005542).
database_cross_reference: FBC:Autogenerated

multi-cell-component structure
type: Class
subclass of: anatomical structure
definition: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
database_cross_reference: CARO:0001000
database_cross_reference: UBERON:0005162
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007060
in subset: larval OF

Axiom
annotated source: multi-cell-component structure
annotated property: definition
annotated target: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

neuroblast MBp
type: Class
subclass of: protocerebral neuroblast
definition: Neuroblast that is the precursor to the Kenyon cells (Kunz et al., 2012). There are four of these per hemisphere and they each arise from a distinct neuroectodermal progenitor and produce morphologically distinct primary lineages (Kunz et al., 2012). They continue to divide from the embryonic to the late pupal stage (Lee et al., 1999; Kunz et al., 2012). All four produce largely identical lineages postembryonically (Ito et al., 2013; Yu et al., 2013), sequentially producing gamma, alpha'/beta' and alpha/beta Kenyon cells (Lee et al., 1999; Kunz et al., 2012). In the adult, each lineage remains distinct within the calyx and pedunculus, but the axons reorganize and intermingle within the lobes (Li et al., 2020).
database_cross_reference: VFB:FBbt_00007113
has exact synonym: MB-Nb
has exact synonym: MBNB
has exact synonym: MBp1-4
has exact synonym: mushroom body neuroblast
has exact synonym: neuroblast MB
has exact synonym: neuroblast MBp
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007113
comment: See Ito et al. (2013) figure S1 for distinction between MBp1-4.

Axiom
annotated source: neuroblast MBp
annotated property: definition
annotated target: Neuroblast that is the precursor to the Kenyon cells (Kunz et al., 2012). There are four of these per hemisphere and they each arise from a distinct neuroectodermal progenitor and produce morphologically distinct primary lineages (Kunz et al., 2012). They continue to divide from the embryonic to the late pupal stage (Lee et al., 1999; Kunz et al., 2012). All four produce largely identical lineages postembryonically (Ito et al., 2013; Yu et al., 2013), sequentially producing gamma, alpha'/beta' and alpha/beta Kenyon cells (Lee et al., 1999; Kunz et al., 2012). In the adult, each lineage remains distinct within the calyx and pedunculus, but the axons reorganize and intermingle within the lobes (Li et al., 2020).
database_cross_reference: FlyBase:FBrf0092568
database_cross_reference: FlyBase:FBrf0111409
database_cross_reference: FlyBase:FBrf0218649
database_cross_reference: FlyBase:FBrf0221412
database_cross_reference: FlyBase:FBrf0221438
database_cross_reference: FlyBase:FBrf0248215

Axiom
annotated source: neuroblast MBp
annotated property: hasExactSynonym
annotated target: MBNB
database_cross_reference: FlyBase:FBrf0218649

Axiom
annotated source: neuroblast MBp
annotated property: hasExactSynonym
annotated target: MBp1-4
database_cross_reference: FlyBase:FBrf0221412

Axiom
annotated source: neuroblast MBp
annotated property: hasExactSynonym
annotated target: neuroblast MB
database_cross_reference: FlyBase:FBrf0221438

Axiom
annotated source: neuroblast MBp
annotated property: hasExactSynonym
annotated target: neuroblast MBp
has synonym type: HARTENSTEIN BRAIN LINEAGE

Axiom
annotated source: neuroblast MBp
annotated property: hasExactSynonym
annotated target: neuroblast MBp
has synonym type: ITO LEE BRAIN LINEAGE

cell body rind of the central nervous system
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: Superficial neuronal layer of the central nervous system, composed of glia and the cell bodies of neurons (soma). The cell body rind lies under the perineurium.
database_cross_reference: VFB:FBbt_00007114
has exact synonym: cortex of the central nervous system
has exact synonym: perikaryal rind
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007114

Axiom
annotated source: cell body rind of the central nervous system
annotated property: definition
annotated target: Superficial neuronal layer of the central nervous system, composed of glia and the cell bodies of neurons (soma). The cell body rind lies under the perineurium.
database_cross_reference: FlyBase:FBrf0239343

Axiom
annotated source: cell body rind of the central nervous system
annotated property: hasExactSynonym
annotated target: perikaryal rind
database_cross_reference: FlyBase:FBrf0207181

larval neuroblast
type: Class
equivalent class: Class
  intersection of: neuroblast
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: neuroblast
subclass of: Restriction
  on property: part of
  some values from: larval central nervous system
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Any neuroblast of the larva.
has broad synonym: embryonic/larval neuroblast
database_cross_reference: VFB:FBbt_00007115
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007115
in subset: cur

Axiom
annotated source: larval neuroblast
annotated property: definition
annotated target: Any neuroblast of the larva.
database_cross_reference: FlyBase:FBrf0047815

presumptive embryonic/larval system
type: Class
equivalent class: Class
  intersection of: non-connected developing system
  intersection of: Restriction
    on property: overlaps
    some values from: embryo
subclass of: developing embryonic structure
subclass of: non-connected developing system
definition: The sum of all the developing presumptive components of a specific embryonic/larval system in an embryo.
database_cross_reference: UBERON:6007116
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007116

Axiom
annotated source: presumptive embryonic/larval system
annotated property: definition
annotated target: The sum of all the developing presumptive components of a specific embryonic/larval system in an embryo.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

sensillum
type: Class
equivalent class: Class
  intersection of: cell cluster organ
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050906
subclass of: sense organ
subclass of: cell cluster organ
definition: A sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organized unit with a largely bona fide boundary.
database_cross_reference: UBERON:0002536
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007152
in subset: FB gloss
in subset: larval OF

Axiom
annotated source: sensillum
annotated property: definition
annotated target: A sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organized unit with a largely bona fide boundary.
database_cross_reference: FlyBase:FBrf0111704

cholinergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0014055
subclass of: CL_0000108
subclass of: neuron
definition: Any neuron (FBbt:00005106) that is capable of some acetylcholine secretion, neurotransmission (GO:0014055).
contributor: Q3074571
date: 2008-05-15T03:05:53Z
database_cross_reference: CL:0000108
database_cross_reference: VFB:FBbt_00007173
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007173
in subset: larval OF

Axiom
annotated source: cholinergic neuron
annotated property: definition
annotated target: Any neuron (FBbt:00005106) that is capable of some acetylcholine secretion, neurotransmission (GO:0014055).
database_cross_reference: FBC:Autogenerated

calyx of larval mushroom body
type: Class
subclass of: mushroom body calyx
subclass of: Restriction
  on property: part of
  some values from: embryonic/larval mushroom body
definition: Calyx of the larval mushroom body. It contains dendrites of the larval Kenyon cells (Masuda-Nakagawa et al., 2009; Saumweber et al., 2018). It is organized into around 34 glomeruli, each innervated by a single projection neuron (Masuda-Nakagawa et al., 2009).
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-09-08T12:52:54Z
database_cross_reference: VFB:FBbt_00007191
database_cross_reference: larvalbrain_neuropil:289
database_cross_reference: larvalbrain_neuropil:467
has exact synonym: MB-C
has exact synonym: larval calyx
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007191
in subset: larval OF

Axiom
annotated source: calyx of larval mushroom body
annotated property: definition
annotated target: Calyx of the larval mushroom body. It contains dendrites of the larval Kenyon cells (Masuda-Nakagawa et al., 2009; Saumweber et al., 2018). It is organized into around 34 glomeruli, each innervated by a single projection neuron (Masuda-Nakagawa et al., 2009).
database_cross_reference: FlyBase:FBrf0208205
database_cross_reference: FlyBase:FBrf0238440

Axiom
annotated source: calyx of larval mushroom body
annotated property: hasExactSynonym
annotated target: MB-C
database_cross_reference: FlyBase:FBrf0211533

GABAergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0061534
subclass of: CL_0000617
subclass of: neuron
definition: Any neuron (FBbt:00005106) that is capable of some gamma-aminobutyric acid secretion, neurotransmission (GO:0061534).
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-09-08T03:36:17Z
database_cross_reference: CL:0000617
database_cross_reference: VFB:FBbt_00007228
has exact synonym: GABA-ergic neuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007228
in subset: larval OF
comment: Some GABAergic neurons express ChAT transcripts (and reporters) at low levels, but do not produce functional enzyme (Lacin et al., 2019 - FBrf0242251).

Axiom
annotated source: GABAergic neuron
annotated property: definition
annotated target: Any neuron (FBbt:00005106) that is capable of some gamma-aminobutyric acid secretion, neurotransmission (GO:0061534).
database_cross_reference: FBC:Autogenerated

cell cluster organ
type: Class
subclass of: multicellular structure
definition: A cluster of cells of various types which form a discrete structure with a largely bona fide boundary.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-10-21T12:18:17Z
database_cross_reference: UBERON:0010001
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007229

Axiom
annotated source: cell cluster organ
annotated property: definition
annotated target: A cluster of cells of various types which form a discrete structure with a largely bona fide boundary.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

internal sensillum
type: Class
subclass of: sensillum
subclass of: internal sense organ
definition: Sensillum that is internal to the animal - i.e. having no part that is part of the cuticle.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-10-21T02:04:23Z
database_cross_reference: UBERON:6007233
database_cross_reference: VFB:FBbt_00007233
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007233

Axiom
annotated source: internal sensillum
annotated property: definition
annotated target: Sensillum that is internal to the animal - i.e. having no part that is part of the cuticle.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

larval sensillum
type: Class
equivalent class: Class
  intersection of: sensillum
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval sense organ
subclass of: sensillum
definition: Any sensillum of the larva.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-10-22T09:42:58Z
database_cross_reference: UBERON:6007240
has exact synonym: embryonic/larval sensillum
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007240

Axiom
annotated source: larval sensillum
annotated property: definition
annotated target: Any sensillum of the larva.
database_cross_reference: FBC:Autogenerated

embryonic/larval head sensillum
type: Class
equivalent class: Class
  intersection of: sensillum
  intersection of: Restriction
    on property: part of
    some values from: larval head
subclass of: head sensillum
subclass of: larval sensillum
subclass of: embryonic/larval head sense organ
definition: Any sensillum (FBbt:00007152) that is part of some larval head (FBbt:00001730).
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-10-22T09:42:58Z
database_cross_reference: UBERON:6007242
has exact synonym: larval head sensillum
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007242

Axiom
annotated source: embryonic/larval head sensillum
annotated property: definition
annotated target: Any sensillum (FBbt:00007152) that is part of some larval head (FBbt:00001730).
database_cross_reference: FBC:Autogenerated

cuticular specialization
type: Class
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: cuticle
definition: Specialized structure that is found on the cuticle.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-10-22T02:20:05Z
database_cross_reference: UBERON:6007245
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007245

Axiom
annotated source: cuticular specialization
annotated property: definition
annotated target: Specialized structure that is found on the cuticle.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

disconnected anatomical group
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all continuous with each other.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-11-04T03:09:28Z
database_cross_reference: UBERON:0034923
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007276

Axiom
annotated source: disconnected anatomical group
annotated property: definition
annotated target: Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all continuous with each other.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

anatomical cluster
type: Class
subclass of: disconnected anatomical group
definition: Anatomical group whose component anatomical structures lie in close proximity to each other.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-11-04T03:13:41Z
database_cross_reference: UBERON:0000477
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007277

Axiom
annotated source: anatomical cluster
annotated property: definition
annotated target: Anatomical group whose component anatomical structures lie in close proximity to each other.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

non-connected functional system
type: Class
subclass of: disconnected anatomical group
definition: An anatomical group whose component structures share a common function.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-11-04T03:18:01Z
database_cross_reference: UBERON:0015203
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007278

Axiom
annotated source: non-connected functional system
annotated property: definition
annotated target: An anatomical group whose component structures share a common function.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

embryonic/larval head sense organ
type: Class
equivalent class: Class
  intersection of: sense organ
  intersection of: Restriction
    on property: part of
    some values from: larval head
subclass of: larval sense organ
subclass of: Restriction
  on property: part of
  some values from: larval head
definition: Any sense organ (FBbt:00005155) that is part of some larval head (FBbt:00001730).
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-11-05T10:34:14Z
database_cross_reference: UBERON:6007280
database_cross_reference: VFB:FBbt_00007280
has exact synonym: larval head sense organ
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007280

Axiom
annotated source: embryonic/larval head sense organ
annotated property: definition
annotated target: Any sense organ (FBbt:00005155) that is part of some larval head (FBbt:00001730).
database_cross_reference: FBC:Autogenerated

integumentary specialization
type: Class
subclass of: anatomical entity
subclass of: Restriction
  on property: part of
  some values from: integumentary system
definition: Specialized structure that is found on the integument.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-11-06T03:13:52Z
database_cross_reference: UBERON:6007288
has exact synonym: integumentary specialisation
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007288

Axiom
annotated source: integumentary specialization
annotated property: definition
annotated target: Specialized structure that is found on the integument.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

organ system subdivision
type: Class
subclass of: multicellular structure
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-12-12T07:22:29Z
database_cross_reference: UBERON:0011216
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007330

segmental subdivision of organ system
type: Class
subclass of: organ system subdivision
definition: The part of some organism that is part of some specified segment.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-12-12T07:22:57Z
database_cross_reference: UBERON:6007331
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007331

Axiom
annotated source: segmental subdivision of organ system
annotated property: definition
annotated target: The part of some organism that is part of some specified segment.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

somatic stem cell
type: Class
subclass of: somatic precursor cell
subclass of: stem cell
definition: Stem cell that is a progenitor of somatic cells.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2009-06-25T05:38:39Z
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007344

Axiom
annotated source: somatic stem cell
annotated property: definition
annotated target: Stem cell that is a progenitor of somatic cells.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

aminergic neuron
type: Class
subclass of: neuron
definition: A neuron that uses a biogenic amine as its neurotransmitter (Vomel and Wegener, 2008; Fuchs et al., 2014).
contributor: https://orcid.org/0000-0002-7073-9172
date: 2009-07-13T04:06:57Z
database_cross_reference: VFB:FBbt_00007368
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007368
comment: Strictly speaking, "aminergic" should refer to any type of amine being used as a neurotransmitter. However, the term is most commonly used to refer to biogenic amines only, which is the meaning we retain here. See https://github.com/geneontology/go-ontology/issues/21625.

Axiom
annotated source: aminergic neuron
annotated property: definition
annotated target: A neuron that uses a biogenic amine as its neurotransmitter (Vomel and Wegener, 2008; Fuchs et al., 2014).
database_cross_reference: FlyBase:FBrf0210246
database_cross_reference: doi:10.1038/srep05526

internal sense organ
type: Class
subclass of: sense organ
definition: Sense organ that is internal to the animal - i.e. having no part that is part of the cuticle.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2009-10-19T02:27:41Z
database_cross_reference: UBERON:6007373
database_cross_reference: VFB:FBbt_00007373
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007373

Axiom
annotated source: internal sense organ
annotated property: definition
annotated target: Sense organ that is internal to the animal - i.e. having no part that is part of the cuticle.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

mushroom body intrinsic neuron
type: Class
equivalent class: Class
  intersection of: intrinsic neuron
  intersection of: Restriction
    on property: has synaptic IO in region
    some values from: mushroom body
subclass of: intrinsic neuron
subclass of: Restriction
  on property: has synaptic IO in region
  some values from: mushroom body
definition: An interneuron that innervates only the mushroom body.
database_cross_reference: VFB:FBbt_00007484
has exact synonym: MBIN
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007484

Axiom
annotated source: mushroom body intrinsic neuron
annotated property: definition
annotated target: An interneuron that innervates only the mushroom body.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: mushroom body intrinsic neuron
annotated property: hasExactSynonym
annotated target: MBIN
database_cross_reference: FlyBase:FBrf0205263

embryonic/larval gut
type: Class
equivalent class: Class
  intersection of: gut
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: gut
subclass of: Restriction
  on property: part of
  some values from: embryonic/larval alimentary canal
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Structure consisting of the embryonic/larval foregut, midgut and hindgut.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2010-10-04T09:58:25Z
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007512

Axiom
annotated source: embryonic/larval gut
annotated property: definition
annotated target: Structure consisting of the embryonic/larval foregut, midgut and hindgut.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

trichome field
type: Class
subclass of: BFO_0000040
subclass of: anatomical cluster
subclass of: Restriction
  on property: composed primarily of
  some values from: trichome
definition: A group of trichomes covering a region of integument.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007658

Axiom
annotated source: trichome field
annotated property: definition
annotated target: A group of trichomes covering a region of integument.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

larval optic anlage
type: Class
subclass of: anlage
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: embryonic/larval optic lobe
subclass of: Restriction
  on property: develops from
  some values from: embryonic optic lobe primordium
definition: An anlage that is a precursor of some part of the adult optic lobe in the larva. It develops from the embryonic optic lobe primordium.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2013-03-13T02:59:16Z
database_cross_reference: VFB:FBbt_00007676
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007676

Axiom
annotated source: larval optic anlage
annotated property: definition
annotated target: An anlage that is a precursor of some part of the adult optic lobe in the larva. It develops from the embryonic optic lobe primordium.
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: https://orcid.org/0000-0002-7073-9172

sensory system
type: Class
equivalent class: Class
  intersection of: non-connected functional system
  intersection of: Restriction
    on property: capable of
    some values from: GO_0007600
subclass of: BFO_0000040
subclass of: non-connected functional system
subclass of: Restriction
  on property: overlaps
  some values from: nervous system
subclass of: Restriction
  on property: capable of
  some values from: GO_0007600
definition: An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception.
database_cross_reference: UBERON:0001032
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007692
in subset: expressionslim flybase ribbon
comment: Note - the relationship of this class to the nervous system is overlap. This allows for sense organ components that function in the transduction of sensory signals but that are not considered to be part of the nervous system to be part of sensory systems.

Axiom
annotated source: sensory system
annotated property: definition
annotated target: An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

sensory system neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of part of
    some values from: GO_0007600
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: sensory system
subclass of: Restriction
  on property: capable of part of
  some values from: GO_0007600
definition: Any neuron (FBbt:00005106) that capable of part of some sensory perception (GO:0007600).
database_cross_reference: VFB:FBbt_00007693
has OBO namespace: fly_anatomy.ontology
id: FBbt:00007693

Axiom
annotated source: sensory system neuron
annotated property: definition
annotated target: Any neuron (FBbt:00005106) that capable of part of some sensory perception (GO:0007600).
database_cross_reference: https://orcid.org/0000-0001-5948-3092

embryonic/larval mushroom body
type: Class
subclass of: mushroom body
subclass of: Restriction
  on property: part of
  some values from: larval protocerebrum
subclass of: Restriction
  on property: part of
  some values from: larval central brain
definition: Mushroom body (MB) of the larva. It only has two lobes, medial and vertical, in contrast to the adult MB, which has five lobes (Lee et al., 1999). Both lobes are composed of gamma neurons, which are the only Kenyon cells (KCs) present in the newly hatched first instar (Kunz et al., 2012). MB neuroblasts continue to produce new KCs throughout the larval stages (Lee et al., 1999). These new KCs form layers in the larval MB peduncle and lobes, with four distinguishable layers present in the third instar (Kurusu et al., 2002). Three types of KCs can be identified in these layers: embryonic-born gamma type (surface layer), larval-born gamma type (outer and inner layers) and larval-born alpha'/beta' type (core layer) neurons (Kurusu et al., 2002). During the pupal stage, alpha/beta KCs are produced and the larval MB is remodeled into the adult MB (Lee et al., 1999).
database_cross_reference: VFB:FBbt_00011929
database_cross_reference: larvalbrain_neuropil:385
database_cross_reference: larvalbrain_neuropil:563
has exact synonym: larval mushroom body
has OBO namespace: fly_anatomy.ontology
id: FBbt:00011929
in subset: cur
in subset: larval OF
comment: The four layers in the pedunculus and lobes were identified by staining with a FasII antibody. The surface layer is partially FasII-negative, the outer and inner layers are FasII-positive and the core is FasII-negative (Selcho et al., 2009; Kurusu et al., 2002).

Axiom
annotated source: embryonic/larval mushroom body
annotated property: definition
annotated target: Mushroom body (MB) of the larva. It only has two lobes, medial and vertical, in contrast to the adult MB, which has five lobes (Lee et al., 1999). Both lobes are composed of gamma neurons, which are the only Kenyon cells (KCs) present in the newly hatched first instar (Kunz et al., 2012). MB neuroblasts continue to produce new KCs throughout the larval stages (Lee et al., 1999). These new KCs form layers in the larval MB peduncle and lobes, with four distinguishable layers present in the third instar (Kurusu et al., 2002). Three types of KCs can be identified in these layers: embryonic-born gamma type (surface layer), larval-born gamma type (outer and inner layers) and larval-born alpha'/beta' type (core layer) neurons (Kurusu et al., 2002). During the pupal stage, alpha/beta KCs are produced and the larval MB is remodeled into the adult MB (Lee et al., 1999).
database_cross_reference: FlyBase:FBrf0111409
database_cross_reference: FlyBase:FBrf0144836
database_cross_reference: FlyBase:FBrf0218649

early extended germ band embryo
type: Class
subclass of: extended germ band embryo
definition: A collective term for stages 9 and 10.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00014201
in subset: cur

Axiom
annotated source: early extended germ band embryo
annotated property: definition
annotated target: A collective term for stages 9 and 10.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

lateral head epidermis primordium
type: Class
subclass of: developing embryonic structure
subclass of: head epidermis primordium
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: extended germ band embryo
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: central brain anlage
subclass of: Restriction
  on property: develops into
  some values from: lateral head epidermis
definition: A(n) primordium that develops into some lateral head epidermis. It develops from some central brain anlage.
has narrow synonym: P1 HeadEpL
has narrow synonym: P2 HeadEpL
has OBO namespace: fly_anatomy.ontology
id: FBbt:00014203
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: lateral head epidermis primordium
annotated property: definition
annotated target: A(n) primordium that develops into some lateral head epidermis. It develops from some central brain anlage.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: lateral head epidermis primordium
annotated property: hasNarrowSynonym
annotated target: P1 HeadEpL
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: lateral head epidermis primordium
annotated property: hasNarrowSynonym
annotated target: P2 HeadEpL
database_cross_reference: https://orcid.org/0000-0002-7073-9172

central brain anlage
type: Class
subclass of: BFO_0000002
subclass of: developing embryonic structure
subclass of: anlage
subclass of: Class
  intersection of: Restriction
    on property: develops into
    some values from: central brain primordium
  intersection of: Restriction
    on property: develops into
    some values from: lateral head epidermis primordium
subclass of: Restriction
  on property: part of
  some values from: procephalic neurogenic region
subclass of: Restriction
  on property: part of
  some values from: gastrula embryo
subclass of: Restriction
  on property: develops from
  some values from: central brain anlage in statu nascendi
definition: Anlage of the embryonic central brain in the gastrula embryo that will give rise to the central brain primordium.
has exact synonym: A CenBr
has OBO namespace: fly_anatomy.ontology
has related synonym: AProcEC
has related synonym: procephalic ectoderm anlage
id: FBbt:00015256
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: central brain anlage
annotated property: definition
annotated target: Anlage of the embryonic central brain in the gastrula embryo that will give rise to the central brain primordium.
database_cross_reference: FBC:VH
database_cross_reference: https://orcid.org/0000-0001-5948-3092

Axiom
annotated source: central brain anlage
annotated property: hasExactSynonym
annotated target: A CenBr
database_cross_reference: https://orcid.org/0000-0002-7073-9172

ventral trunk epidermis primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: late extended germ band embryo
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: ventral epidermis primordium
subclass of: Restriction
  on property: develops into
  some values from: embryonic ventral trunk epidermis
definition: Primordium of the ventral trunk epidermis of the late extended germ band and dorsal closure embryo that will give rise to the embryonic ventral trunk epidermis.
has exact synonym: P1 VenEp
has OBO namespace: fly_anatomy.ontology
id: FBbt:00016007
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: ventral trunk epidermis primordium
annotated property: definition
annotated target: Primordium of the ventral trunk epidermis of the late extended germ band and dorsal closure embryo that will give rise to the embryonic ventral trunk epidermis.
database_cross_reference: FBC:VH

Axiom
annotated source: ventral trunk epidermis primordium
annotated property: hasExactSynonym
annotated target: P1 VenEp
database_cross_reference: https://orcid.org/0000-0002-7073-9172

anal pad primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: late extended germ band embryo
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: ventral epidermis primordium
subclass of: Restriction
  on property: develops into
  some values from: embryonic anal pad
definition: Primordium of the anal pad of the late extended germ band and dorsal closure embryo that will give rise to the embryonic anal pads.
has OBO namespace: fly_anatomy.ontology
has related synonym: A/P1 AnPd
has related synonym: anal pad specific anlage
id: FBbt:00016008
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: anal pad primordium
annotated property: definition
annotated target: Primordium of the anal pad of the late extended germ band and dorsal closure embryo that will give rise to the embryonic anal pads.
database_cross_reference: FBC:VH

Axiom
annotated source: anal pad primordium
annotated property: hasRelatedSynonym
annotated target: A/P1 AnPd
database_cross_reference: https://orcid.org/0000-0002-7073-9172

ventral apodeme anlage
type: Class
subclass of: developing embryonic structure
subclass of: anlage
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: late extended germ band embryo
subclass of: Restriction
  on property: develops from
  some values from: ventral epidermis primordium
subclass of: Restriction
  on property: develops into
  some values from: ventral apodeme primordium
definition: Anlage of the ventral apodeme of the late extended germ band embryo that will give rise to the ventral apodeme primordium.
has exact synonym: A venApo
has OBO namespace: fly_anatomy.ontology
id: FBbt:00016009
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: ventral apodeme anlage
annotated property: definition
annotated target: Anlage of the ventral apodeme of the late extended germ band embryo that will give rise to the ventral apodeme primordium.
database_cross_reference: FBC:VH

Axiom
annotated source: ventral apodeme anlage
annotated property: hasExactSynonym
annotated target: A venApo
database_cross_reference: https://orcid.org/0000-0002-7073-9172

ventral apodeme primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: ventral apodeme anlage
subclass of: Restriction
  on property: develops into
  some values from: embryonic ventral apodeme
definition: Primordium of the ventral apodeme of the dorsal closure embryo that will give rise to the ventral apodemes.
has exact synonym: P1 venApo
has OBO namespace: fly_anatomy.ontology
has related synonym: ventral apodeme specific primordium
id: FBbt:00016010
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: ventral apodeme primordium
annotated property: definition
annotated target: Primordium of the ventral apodeme of the dorsal closure embryo that will give rise to the ventral apodemes.
database_cross_reference: FBC:VH

Axiom
annotated source: ventral apodeme primordium
annotated property: hasExactSynonym
annotated target: P1 venApo
database_cross_reference: https://orcid.org/0000-0002-7073-9172

denticle field primordium
type: Class
subclass of: developing embryonic structure
subclass of: primordium
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: dorsal closure embryo
subclass of: Restriction
  on property: develops from
  some values from: denticle field anlage
subclass of: Restriction
  on property: develops into
  some values from: denticle field
definition: Primordium of the denticle field of the dorsal closure embryo that will give rise to the larval denticle fields.
has exact synonym: P DenBl
has OBO namespace: fly_anatomy.ontology
id: FBbt:00016011
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: denticle field primordium
annotated property: definition
annotated target: Primordium of the denticle field of the dorsal closure embryo that will give rise to the larval denticle fields.
database_cross_reference: FBC:VH

Axiom
annotated source: denticle field primordium
annotated property: hasExactSynonym
annotated target: P DenBl
database_cross_reference: https://orcid.org/0000-0002-7073-9172

denticle field
type: Class
subclass of: trichome field
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: embryonic/larval cuticle
subclass of: Restriction
  on property: develops from
  some values from: denticle field primordium
definition: Region of embryonic and larval ventral cuticle that displays denticle belts. It develops from the denticle field primordium.
has OBO namespace: fly_anatomy.ontology
id: FBbt:00016012
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: denticle field
annotated property: definition
annotated target: Region of embryonic and larval ventral cuticle that displays denticle belts. It develops from the denticle field primordium.
database_cross_reference: FBC:VH
database_cross_reference: FlyBase:FBrf0089570

ectodermal derivative
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: develops from
    some values from: ectoderm
subclass of: germ layer derivative
subclass of: Restriction
  on property: develops from
  some values from: ectoderm
definition: Any anatomical entity (FBbt:10000000) that develops from some ectoderm (FBbt:00000111).
has alternative id: FBbt:00005253
has OBO namespace: fly_anatomy.ontology
id: FBbt:00025990
in subset: cur

Axiom
annotated source: ectodermal derivative
annotated property: definition
annotated target: Any anatomical entity (FBbt:10000000) that develops from some ectoderm (FBbt:00000111).
database_cross_reference: FlyBase:FBrf0043441
database_cross_reference: FlyBase:FBrf0053832

anterior ectoderm derivative
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: develops from
    some values from: anterior ectoderm
subclass of: ectodermal derivative
subclass of: Restriction
  on property: develops from
  some values from: anterior ectoderm
definition: Any anatomical entity (FBbt:10000000) that develops from some anterior ectoderm (FBbt:00000119).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00025991
in subset: cur

Axiom
annotated source: anterior ectoderm derivative
annotated property: definition
annotated target: Any anatomical entity (FBbt:10000000) that develops from some anterior ectoderm (FBbt:00000119).
database_cross_reference: https://orcid.org/0000-0002-7073-9172

ventral ectoderm derivative
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: develops from
    some values from: ventral ectoderm
subclass of: ectodermal derivative
subclass of: Restriction
  on property: develops from
  some values from: ventral ectoderm
definition: Any anatomical entity (FBbt:10000000) that develops from some ventral ectoderm (FBbt:00005558).
has OBO namespace: fly_anatomy.ontology
id: FBbt:00025993
in subset: cur

Axiom
annotated source: ventral ectoderm derivative
annotated property: definition
annotated target: Any anatomical entity (FBbt:10000000) that develops from some ventral ectoderm (FBbt:00005558).
database_cross_reference: https://orcid.org/0000-0002-7073-9172

non-connected developing system
type: Class
subclass of: developing material anatomical entity
subclass of: disconnected anatomical group
definition: The sum of all the anlagen and primordia that will develop into a single system.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2010-04-29T07:57:11Z
database_cross_reference: UBERON:6040003
has OBO namespace: fly_anatomy.ontology
id: FBbt:00040003
comment: Note - this may be the precursor of a connected system that starts out non-connected, such as the tracheal system, or of a system that remains disconnected, e.g. functionally defined systems such as the endocrine system.

Axiom
annotated source: non-connected developing system
annotated property: definition
annotated target: The sum of all the anlagen and primordia that will develop into a single system.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

synaptic neuropil
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: part of
  some values from: neuropil
definition: The part of the neuropil consisting largely of synapsing neuron projections.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2009-08-12T06:32:24Z
database_cross_reference: UBERON:6040005
database_cross_reference: VFB:FBbt_00040005
has OBO namespace: fly_anatomy.ontology
id: FBbt:00040005

Axiom
annotated source: synaptic neuropil
annotated property: definition
annotated target: The part of the neuropil consisting largely of synapsing neuron projections.
database_cross_reference: FlyBase:FBrf0224194

synaptic neuropil domain
type: Class
subclass of: multi-cell-component structure
subclass of: synaptic neuropil
subclass of: Restriction
  on property: part of
  some values from: synaptic neuropil
definition: Region of synaptic neuropil whose boundaries are largely discontinuities in the density of presynaptic terminals: high density in the synaptic neuropil domain, lower or zero density outside this region. These boundaries often correspond to a boundary with glial sheath, tract neuropil or cortex.
date: 2009-12-09T05:03:55Z
database_cross_reference: UBERON:6040007
database_cross_reference: VFB:FBbt_00040007
has OBO namespace: fly_anatomy.ontology
has related synonym: fibrous neuropil
has related synonym: synaptic neuropil
id: FBbt:00040007
in subset: cur
in subset: larval OF

Axiom
annotated source: synaptic neuropil domain
annotated property: definition
annotated target: Region of synaptic neuropil whose boundaries are largely discontinuities in the density of presynaptic terminals: high density in the synaptic neuropil domain, lower or zero density outside this region. These boundaries often correspond to a boundary with glial sheath, tract neuropil or cortex.
database_cross_reference: FlyBase:FBrf0155900
database_cross_reference: FlyBase:FBrf0224194
database_cross_reference: FlyBase:FBrf0237252

synaptic neuropil block
type: Class
subclass of: disconnected anatomical group
subclass of: synaptic neuropil
subclass of: Restriction
  on property: part of
  some values from: synaptic neuropil
definition: A closely associated group of synaptic neuropil domains.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2009-08-12T04:30:28Z
database_cross_reference: UBERON:6041000
database_cross_reference: VFB:FBbt_00041000
has exact synonym: level 1 neuropil
has OBO namespace: fly_anatomy.ontology
id: FBbt:00041000

Axiom
annotated source: synaptic neuropil block
annotated property: definition
annotated target: A closely associated group of synaptic neuropil domains.
database_cross_reference: FBC:KI
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: synaptic neuropil block
annotated property: hasExactSynonym
annotated target: level 1 neuropil
database_cross_reference: FlyBase:FBrf0224194

gut
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part of
  some values from: alimentary canal
definition: Structure consisting of a simple epithelium surrounded by visceral muscles, nerves and tracheae. The gut is divided into foregut, midgut and hindgut regions, based on developmental origin.
contributor: https://orcid.org/0000-0002-1373-1705
has OBO namespace: fly_anatomy.ontology
id: FBbt:00047143

Axiom
annotated source: gut
annotated property: definition
annotated target: Structure consisting of a simple epithelium surrounded by visceral muscles, nerves and tracheae. The gut is divided into foregut, midgut and hindgut regions, based on developmental origin.
database_cross_reference: FlyBase:FBrf0223413

imaginal tissue
type: Class
subclass of: developing material anatomical entity
definition: Any group of similar imaginal cells, such as an imaginal disc, imaginal ring or imaginal island, or a precursor tissue that forms one of them. These tissues develop separately from other embryonic and larval tissues and they generate adult structures during metamorphosis.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2018-08-15T09:31:08Z
has exact synonym: imaginal structure
has OBO namespace: fly_anatomy.ontology
id: FBbt:00047552
in subset: expressionslim flybase ribbon

Axiom
annotated source: imaginal tissue
annotated property: definition
annotated target: Any group of similar imaginal cells, such as an imaginal disc, imaginal ring or imaginal island, or a precursor tissue that forms one of them. These tissues develop separately from other embryonic and larval tissues and they generate adult structures during metamorphosis.
database_cross_reference: FlyBase:FBrf0064789

Axiom
annotated source: imaginal tissue
annotated property: hasExactSynonym
annotated target: imaginal structure
database_cross_reference: FlyBase:FBrf0053815

visual system
type: Class
equivalent class: Class
  intersection of: non-connected functional system
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050953
subclass of: sensory system
subclass of: Restriction
  on property: capable of
  some values from: GO_0050953
definition: An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of light.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2018-09-18T13:08:28Z
has OBO namespace: fly_anatomy.ontology
id: FBbt:00047735

Axiom
annotated source: visual system
annotated property: definition
annotated target: An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of light.
database_cross_reference: https://orcid.org/0000-0002-1373-1705

visual system neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of part of
    some values from: GO_0050953
subclass of: sensory system neuron
subclass of: Restriction
  on property: part of
  some values from: visual system
subclass of: Restriction
  on property: capable of part of
  some values from: GO_0050953
definition: Any neuron (FBbt:00005106) that capable of part of some sensory perception of light stimulus (GO:0050953).
contributor: https://orcid.org/0000-0002-1373-1705
date: 2018-09-18T13:09:24Z
database_cross_reference: VFB:FBbt_00047736
has OBO namespace: fly_anatomy.ontology
id: FBbt:00047736

Axiom
annotated source: visual system neuron
annotated property: definition
annotated target: Any neuron (FBbt:00005106) that capable of part of some sensory perception of light stimulus (GO:0050953).
database_cross_reference: https://orcid.org/0000-0002-1373-1705

embryonic/larval lateral glial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: part of
    some values from: larval nervous system
  intersection of: Restriction
    on property: expresses
    some values from: FBgn0011701
subclass of: larval glial cell
subclass of: Restriction
  on property: expresses
  some values from: FBgn0011701
definition: Any glial cell of the embryo or larva that derives from the neurogenic region of the ectoderm. Their identity is established by the expression of the gene glial cells missing (gcm), which results in expression of reversed polarity (repo), often used as a marker for lateral glia (Jacobs, 2000). This includes perineurial and subperineurial glia of the central and peripheral nervous systems, cell body (cortex) glia, wrapping glia and some of the neuropil associated glia (Beckervordersandforth et al., 2008). There are around 25 of these per abdominal hemisegment in a stage 16 embryo (Beckervordersandforth et al., 2008).
contributor: https://orcid.org/0000-0002-1373-1705
date: 2018-10-22T12:36:01Z
database_cross_reference: VFB:FBbt_00047861
has OBO namespace: fly_anatomy.ontology
id: FBbt:00047861

Axiom
annotated source: embryonic/larval lateral glial cell
annotated property: definition
annotated target: Any glial cell of the embryo or larva that derives from the neurogenic region of the ectoderm. Their identity is established by the expression of the gene glial cells missing (gcm), which results in expression of reversed polarity (repo), often used as a marker for lateral glia (Jacobs, 2000). This includes perineurial and subperineurial glia of the central and peripheral nervous systems, cell body (cortex) glia, wrapping glia and some of the neuropil associated glia (Beckervordersandforth et al., 2008). There are around 25 of these per abdominal hemisegment in a stage 16 embryo (Beckervordersandforth et al., 2008).
database_cross_reference: FlyBase:FBrf0128507
database_cross_reference: FlyBase:FBrf0205499

central brain
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part of
  some values from: brain
definition: Brain excluding the optic lobes.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2018-10-24T15:11:55Z
database_cross_reference: VFB:FBbt_00047888
has OBO namespace: fly_anatomy.ontology
id: FBbt:00047888

Axiom
annotated source: central brain
annotated property: definition
annotated target: Brain excluding the optic lobes.
database_cross_reference: FlyBase:FBrf0224194
database_cross_reference: https://orcid.org/0000-0002-1373-1705

larval central brain
type: Class
subclass of: central brain
subclass of: Restriction
  on property: part of
  some values from: larval brain
definition: Larval brain excluding the optic lobes.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2018-10-24T15:12:43Z
database_cross_reference: VFB:FBbt_00047889
has OBO namespace: fly_anatomy.ontology
id: FBbt:00047889

Axiom
annotated source: larval central brain
annotated property: definition
annotated target: Larval brain excluding the optic lobes.
database_cross_reference: https://orcid.org/0000-0002-1373-1705

cell body rind of larval mushroom body
type: Class
subclass of: cell body rind region
subclass of: Restriction
  on property: part of
  some values from: cell body rind of larval protocerebrum
subclass of: Restriction
  on property: continuous with
  some values from: embryonic/larval mushroom body
definition: Region of the cell body rind overlying the larval mushroom body.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2018-11-15T10:26:28Z
database_cross_reference: VFB:FBbt_00047951
has exact synonym: larval mushroom body cortex
has OBO namespace: fly_anatomy.ontology
id: FBbt:00047951

Axiom
annotated source: cell body rind of larval mushroom body
annotated property: definition
annotated target: Region of the cell body rind overlying the larval mushroom body.
database_cross_reference: https://orcid.org/0000-0002-1373-1705

cell body rind of larval central nervous system
type: Class
subclass of: cell body rind of the central nervous system
subclass of: Restriction
  on property: part of
  some values from: larval central nervous system
definition: Superficial layer of neuronal cell bodies and glia that overlies the neuropil of the larval central nervous system.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2020-06-15T13:37:38Z
database_cross_reference: VFB:FBbt_00049602
has exact synonym: larval cortex
has OBO namespace: fly_anatomy.ontology
id: FBbt:00049602

Axiom
annotated source: cell body rind of larval central nervous system
annotated property: definition
annotated target: Superficial layer of neuronal cell bodies and glia that overlies the neuropil of the larval central nervous system.
database_cross_reference: https://orcid.org/0000-0002-1373-1705

larval brain cell body glial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: part of
    some values from: cell body rind of larval brain
subclass of: embryonic/larval cell body glial cell
subclass of: Restriction
  on property: part of
  some values from: cell body rind of larval brain
definition: Glial cell located amongst neuronal cell bodies in the cortex of the embryonic/larval brain.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2020-06-15T14:20:49Z
database_cross_reference: VFB:FBbt_00049604
has exact synonym: embryonic/larval brain cortex glial cell
has exact synonym: larval brain CBG
has OBO namespace: fly_anatomy.ontology
id: FBbt:00049604

Axiom
annotated source: larval brain cell body glial cell
annotated property: definition
annotated target: Glial cell located amongst neuronal cell bodies in the cortex of the embryonic/larval brain.
database_cross_reference: FlyBase:FBrf0237238

undifferentiated glial cell
type: Class
subclass of: glial cell
definition: Glial cell that has not differentiated into a stable specialist fate. These cells may be migratory and/or phagocytic (Edwards and Meinertzhagen, 2010; Shklyar et al., 2014).
contributor: https://orcid.org/0000-0002-1373-1705
date: 2020-06-18T10:07:15Z
database_cross_reference: VFB:FBbt_00049609
has exact synonym: developing glial cell
has exact synonym: udg
has OBO namespace: fly_anatomy.ontology
id: FBbt:00049609

Axiom
annotated source: undifferentiated glial cell
annotated property: definition
annotated target: Glial cell that has not differentiated into a stable specialist fate. These cells may be migratory and/or phagocytic (Edwards and Meinertzhagen, 2010; Shklyar et al., 2014).
database_cross_reference: FlyBase:FBrf0210316
database_cross_reference: FlyBase:FBrf0225975

Axiom
annotated source: undifferentiated glial cell
annotated property: hasExactSynonym
annotated target: developing glial cell
database_cross_reference: FlyBase:FBrf0225975

Axiom
annotated source: undifferentiated glial cell
annotated property: hasExactSynonym
annotated target: udg
database_cross_reference: FlyBase:FBrf0210316

mushroom body neuropil subdivision
type: Class
equivalent class: Class
  intersection of: synaptic neuropil
  intersection of: Restriction
    on property: part of
    some values from: mushroom body
subclass of: synaptic neuropil
subclass of: Restriction
  on property: part of
  some values from: mushroom body
definition: Any synaptic neuropil (FBbt:00040005) that is part of some mushroom body (FBbt:00005801).
contributor: https://orcid.org/0000-0002-1373-1705
date: 2020-09-29T13:11:07Z
database_cross_reference: VFB:FBbt_00049824
has OBO namespace: fly_anatomy.ontology
id: FBbt:00049824

Axiom
annotated source: mushroom body neuropil subdivision
annotated property: definition
annotated target: Any synaptic neuropil (FBbt:00040005) that is part of some mushroom body (FBbt:00005801).
database_cross_reference: FBC:Autogenerated

larval Kenyon cell
type: Class
equivalent class: Class
  intersection of: Kenyon cell
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: supraesophageal ganglion neuron
subclass of: Kenyon cell
subclass of: larval interneuron
subclass of: Restriction
  on property: part of
  some values from: larval brain
subclass of: Restriction
  on property: has soma location
  some values from: cell body rind of larval mushroom body
subclass of: Restriction
  on property: overlaps
  some values from: pedunculus of larval mushroom body
subclass of: Restriction
  on property: receives synaptic input in region
  some values from: calyx of larval mushroom body
subclass of: Restriction
  on property: sends synaptic output to region
  some values from: medial lobe of larval mushroom body
subclass of: Restriction
  on property: sends synaptic output to region
  some values from: vertical lobe of larval mushroom body
definition: Kenyon cell (KC) of the larval (or late embryonic) mushroom body. It has its soma in the mushroom body cell body rind (above the calyx) and dendrites in the calyx and its axon projects through the pedunculus and bifurcates into the vertical and medial lobes (Lee et al., 1999). The first KCs generated in the embryo and early larva are gamma neurons, with alpha'/beta' neurons being born in the late larva (Lee et al., 1999; Kunz et al., 2012). Later born neurons occupy more central positions within the pedunculus and lobe bundles, so that in the late third instar, the embryonic gamma axons occupy the periphery, with the larval-born gamma neurons beneath, and the alpha'/beta' neurons at the core (Kurusu et al., 2002). During the pupal stage, gamma KCs are dramatically remodeled to form the adult gamma lobe, alpha'/beta' KCs remain largely the same and alpha/beta neurons are generated to form the alpha and beta lobes (Lee et al., 1999).
contributor: https://orcid.org/0000-0002-1373-1705
date: 2020-09-30T09:55:32Z
database_cross_reference: VFB:FBbt_00049826
has exact synonym: embryonic/larval KC
has exact synonym: embryonic/larval Kenyon cell
has exact synonym: larval KC
has OBO namespace: fly_anatomy.ontology
id: FBbt:00049826

Axiom
annotated source: larval Kenyon cell
annotated property: definition
annotated target: Kenyon cell (KC) of the larval (or late embryonic) mushroom body. It has its soma in the mushroom body cell body rind (above the calyx) and dendrites in the calyx and its axon projects through the pedunculus and bifurcates into the vertical and medial lobes (Lee et al., 1999). The first KCs generated in the embryo and early larva are gamma neurons, with alpha'/beta' neurons being born in the late larva (Lee et al., 1999; Kunz et al., 2012). Later born neurons occupy more central positions within the pedunculus and lobe bundles, so that in the late third instar, the embryonic gamma axons occupy the periphery, with the larval-born gamma neurons beneath, and the alpha'/beta' neurons at the core (Kurusu et al., 2002). During the pupal stage, gamma KCs are dramatically remodeled to form the adult gamma lobe, alpha'/beta' KCs remain largely the same and alpha/beta neurons are generated to form the alpha and beta lobes (Lee et al., 1999).
database_cross_reference: FlyBase:FBrf0111409
database_cross_reference: FlyBase:FBrf0144836
database_cross_reference: FlyBase:FBrf0218649

Axiom
annotated source: larval Kenyon cell
annotated property: hasExactSynonym
annotated target: larval KC
database_cross_reference: FlyBase:FBrf0227179

supraesophageal zone
type: Class
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: supraesophageal ganglion
definition: Neuropil mass above the esophagus (Ito et al., 2014). It is part of the cerebral (supraesophageal) ganglion (Ito et al., 2014).
contributor: https://orcid.org/0000-0002-1373-1705
date: 2021-02-26T13:05:56Z
has broad synonym: supraesophageal ganglion
database_cross_reference: VFB:FBbt_00051069
has exact synonym: SPZ
has OBO namespace: fly_anatomy.ontology
id: FBbt:00051069

Axiom
annotated source: supraesophageal zone
annotated property: definition
annotated target: Neuropil mass above the esophagus (Ito et al., 2014). It is part of the cerebral (supraesophageal) ganglion (Ito et al., 2014).
database_cross_reference: FlyBase:FBrf0224194

Axiom
annotated source: supraesophageal zone
annotated property: hasExactSynonym
annotated target: SPZ
database_cross_reference: FlyBase:FBrf0224194

larval supraesophageal zone
type: Class
equivalent class: Class
  intersection of: supraesophageal zone
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: supraesophageal zone
subclass of: Restriction
  on property: part of
  some values from: larval brain
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: Neuropil mass above the larval esophagus consisting of the protocerebral and deutocerebral neuromeres and part of the tritocerebrum.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2021-02-26T13:07:57Z
has broad synonym: larval supraesophageal ganglion
database_cross_reference: VFB:FBbt_00051070
has exact synonym: larval SPZ
has OBO namespace: fly_anatomy.ontology
id: FBbt:00051070
comment: This is analogous to the adult term based on Ito et al. (2014), reflecting location relative to the esophagus, rather than segmental identity.

Axiom
annotated source: larval supraesophageal zone
annotated property: definition
annotated target: Neuropil mass above the larval esophagus consisting of the protocerebral and deutocerebral neuromeres and part of the tritocerebrum.
database_cross_reference: FlyBase:FBrf0224194

local neuron
type: Class
subclass of: interneuron
definition: Neuron of the central nervous system that has the majority of its inputs and outputs in close proximity within the same region of the neuropil. Some arbors may spread outside of the region, but without sufficient polarity to define the neuron as an input or output neuron.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2021-09-22T08:47:38Z
database_cross_reference: VFB:FBbt_00051493
has exact synonym: local interneuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00051493

Axiom
annotated source: local neuron
annotated property: definition
annotated target: Neuron of the central nervous system that has the majority of its inputs and outputs in close proximity within the same region of the neuropil. Some arbors may spread outside of the region, but without sufficient polarity to define the neuron as an input or output neuron.
database_cross_reference: FlyBase:FBrf0232785
database_cross_reference: FlyBase:FBrf0242477

larval interneuron
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: interneuron
subclass of: larval CNS neuron
subclass of: Restriction
  on property: part of
  some values from: larval central nervous system
subclass of: Restriction
  on property: has soma location
  some values from: cell body rind of larval central nervous system
definition: Any interneuron of the larva.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2022-01-13T15:32:23Z
database_cross_reference: VFB:FBbt_00052047
has OBO namespace: fly_anatomy.ontology
id: FBbt:00052047

Axiom
annotated source: larval interneuron
annotated property: definition
annotated target: Any interneuron of the larva.
database_cross_reference: FBC:Autogenerated

cell body rind of larval deutocerebrum
type: Class
subclass of: cell body rind region
subclass of: Restriction
  on property: part of
  some values from: larval deutocerebrum
subclass of: Restriction
  on property: part of
  some values from: cell body rind of larval brain
definition: Region of the larval cell body rind that overlies the neuropil of the larval deutocerebrum.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2022-01-14T10:45:19Z
database_cross_reference: VFB:FBbt_00052050
has OBO namespace: fly_anatomy.ontology
id: FBbt:00052050

Axiom
annotated source: cell body rind of larval deutocerebrum
annotated property: definition
annotated target: Region of the larval cell body rind that overlies the neuropil of the larval deutocerebrum.
database_cross_reference: https://orcid.org/0000-0002-1373-1705

cell body rind of larval protocerebrum
type: Class
subclass of: cell body rind region
subclass of: Restriction
  on property: part of
  some values from: larval protocerebrum
subclass of: Restriction
  on property: part of
  some values from: cell body rind of larval brain
definition: Region of the larval cell body rind that overlies the neuropil of the larval protocerebrum.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2022-01-14T10:45:44Z
database_cross_reference: VFB:FBbt_00052051
has OBO namespace: fly_anatomy.ontology
id: FBbt:00052051

Axiom
annotated source: cell body rind of larval protocerebrum
annotated property: definition
annotated target: Region of the larval cell body rind that overlies the neuropil of the larval protocerebrum.
database_cross_reference: https://orcid.org/0000-0002-1373-1705

gut-innervating neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: overlaps
    some values from: gut
subclass of: neuron
subclass of: Restriction
  on property: overlaps
  some values from: gut
definition: Neuron that innervates any part of the gut. These cells include sensory neurons, as well as efferent neurons that terminate on the visceral muscles and the underlying epithelium (Lemaitre and Miguel-Aliaga, 2013). They are chemically and neuroanatomically diverse, with efferent neurons collectively producing several neuropeptides and serotonin (Lemaitre and Miguel-Aliaga, 2013).
contributor: https://orcid.org/0000-0002-1373-1705
date: 2022-03-24T13:50:11Z
database_cross_reference: VFB:FBbt_00052149
has narrow synonym: enteric neuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00052149
comment: Many recent papers do not count the pharyngeal and labral taste neurons as 'enteric neurons', hence only a narrow synonym.

Axiom
annotated source: gut-innervating neuron
annotated property: definition
annotated target: Neuron that innervates any part of the gut. These cells include sensory neurons, as well as efferent neurons that terminate on the visceral muscles and the underlying epithelium (Lemaitre and Miguel-Aliaga, 2013). They are chemically and neuroanatomically diverse, with efferent neurons collectively producing several neuropeptides and serotonin (Lemaitre and Miguel-Aliaga, 2013).
database_cross_reference: FlyBase:FBrf0223413

larval gut-innervating neuron
type: Class
equivalent class: Class
  intersection of: gut-innervating neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuron
subclass of: gut-innervating neuron
subclass of: Restriction
  on property: overlaps
  some values from: embryonic/larval gut
definition: Any gut-innervating neuron of the larva.
contributor: https://orcid.org/0000-0002-1373-1705
date: 2022-03-24T14:16:12Z
database_cross_reference: VFB:FBbt_00052151
has narrow synonym: larval enteric neuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00052151

Axiom
annotated source: larval gut-innervating neuron
annotated property: definition
annotated target: Any gut-innervating neuron of the larva.
database_cross_reference: FlyBase:FBrf0223413

embryonic glial cell
type: Class
subclass of: undifferentiated glial cell
subclass of: Restriction
  on property: part of
  some values from: presumptive embryonic/larval nervous system
definition: Glial cell of the embryo that has not yet reached its mature larval form. These cells may further divide (or die), migrate or extend processes prior to adopting their mature larval forms, positions and numbers (Ito et al., 1995).
contributor: https://orcid.org/0000-0002-1373-1705
date: 2022-10-26T15:19:19Z
database_cross_reference: VFB:FBbt_00052369
has OBO namespace: fly_anatomy.ontology
id: FBbt:00052369

Axiom
annotated source: embryonic glial cell
annotated property: definition
annotated target: Glial cell of the embryo that has not yet reached its mature larval form. These cells may further divide (or die), migrate or extend processes prior to adopting their mature larval forms, positions and numbers (Ito et al., 1995).
database_cross_reference: FlyBase:FBrf0082171

anterior-posterior subdivision of organism
type: Class
subclass of: organism subdivision
contributor: https://orcid.org/0000-0002-7073-9172
date: 2008-06-30T04:15:23Z
database_cross_reference: UBERON:6057001
has OBO namespace: fly_anatomy.ontology
id: FBbt:00057001
in subset: larval OF

larval aminergic neuron
type: Class
equivalent class: Class
  intersection of: aminergic neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuron
subclass of: aminergic neuron
definition: Any aminergic neuron of the larva.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2021-06-03T18:57:00Z
database_cross_reference: VFB:FBbt_00058211
has OBO namespace: fly_anatomy.ontology
id: FBbt:00058211
in subset: cur

Axiom
annotated source: larval aminergic neuron
annotated property: definition
annotated target: Any aminergic neuron of the larva.
database_cross_reference: FBC:Autogenerated

larval peptidergic neuron
type: Class
equivalent class: Class
  intersection of: peptidergic neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuron
subclass of: peptidergic neuron
definition: Any peptidergic neuron of the larva.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2021-06-03T18:57:00Z
database_cross_reference: VFB:FBbt_00058212
has OBO namespace: fly_anatomy.ontology
id: FBbt:00058212
in subset: cur

Axiom
annotated source: larval peptidergic neuron
annotated property: definition
annotated target: Any peptidergic neuron of the larva.
database_cross_reference: FBC:Autogenerated

larval cholinergic neuron
type: Class
equivalent class: Class
  intersection of: cholinergic neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuron
subclass of: cholinergic neuron
definition: Any cholinergic neuron of the larva.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2021-06-03T18:57:00Z
database_cross_reference: VFB:FBbt_00058215
has OBO namespace: fly_anatomy.ontology
id: FBbt:00058215
in subset: cur

Axiom
annotated source: larval cholinergic neuron
annotated property: definition
annotated target: Any cholinergic neuron of the larva.
database_cross_reference: FBC:Autogenerated

larval GABAergic neuron
type: Class
equivalent class: Class
  intersection of: GABAergic neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuron
subclass of: GABAergic neuron
definition: Any GABAergic neuron of the larva.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2021-06-03T18:57:00Z
database_cross_reference: VFB:FBbt_00058217
has OBO namespace: fly_anatomy.ontology
id: FBbt:00058217
in subset: cur

Axiom
annotated source: larval GABAergic neuron
annotated property: definition
annotated target: Any GABAergic neuron of the larva.
database_cross_reference: FBC:Autogenerated

larval glutamatergic neuron
type: Class
equivalent class: Class
  intersection of: glutamatergic neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuron
subclass of: glutamatergic neuron
definition: Any glutamatergic neuron of the larva.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2021-06-03T18:57:00Z
database_cross_reference: VFB:FBbt_00058218
has OBO namespace: fly_anatomy.ontology
id: FBbt:00058218
in subset: cur

Axiom
annotated source: larval glutamatergic neuron
annotated property: definition
annotated target: Any glutamatergic neuron of the larva.
database_cross_reference: FBC:Autogenerated

embryonic/larval sensory neuron
type: Class
equivalent class: Class
  intersection of: larval neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050906
subclass of: larval neuron
subclass of: sensory neuron
definition: Any larval neuron (FBbt:00001446) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
contributor: https://orcid.org/0000-0002-6095-8718
date: 2021-09-27T12:17:06Z
database_cross_reference: VFB:FBbt_00058245
has exact synonym: larval SN
has OBO namespace: fly_anatomy.ontology
id: FBbt:00058245
in subset: cur

Axiom
annotated source: embryonic/larval sensory neuron
annotated property: definition
annotated target: Any larval neuron (FBbt:00001446) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: embryonic/larval sensory neuron
annotated property: hasExactSynonym
annotated target: larval SN
database_cross_reference: FlyBase:FBrf0253566

larval PNS glial cell
type: Class
equivalent class: Class
  intersection of: PNS glial cell
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval glial cell
subclass of: PNS glial cell
subclass of: Restriction
  on property: part of
  some values from: larval peripheral nervous system
definition: Any PNS glial cell of the larva.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2021-09-27T16:42:39Z
database_cross_reference: VFB:FBbt_00058259
has exact synonym: embryonic/larval PNS glial cell
has OBO namespace: fly_anatomy.ontology
id: FBbt:00058259
in subset: cur

Axiom
annotated source: larval PNS glial cell
annotated property: definition
annotated target: Any PNS glial cell of the larva.
database_cross_reference: FBC:Autogenerated

CNS neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: has soma location
    some values from: central nervous system
subclass of: neuron
subclass of: Restriction
  on property: has soma location
  some values from: central nervous system
definition: Any neuron that has its soma in the central nervous system.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2023-11-09T16:06:03Z
database_cross_reference: VFB:FBbt_00059271
has exact synonym: central nervous system neuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00059271
in subset: cur

Axiom
annotated source: CNS neuron
annotated property: definition
annotated target: Any neuron that has its soma in the central nervous system.
database_cross_reference: https://orcid.org/0000-0002-6095-8718

PNS neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: has soma location
    some values from: peripheral nervous system
subclass of: neuron
subclass of: Restriction
  on property: has soma location
  some values from: peripheral nervous system
definition: Any neuron that has its soma in the peripheral nervous system.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2023-11-09T16:08:28Z
database_cross_reference: VFB:FBbt_00059272
has exact synonym: peripheral nervous system neuron
has OBO namespace: fly_anatomy.ontology
has related synonym: afferent neuron
id: FBbt:00059272
in subset: cur

Axiom
annotated source: PNS neuron
annotated property: definition
annotated target: Any neuron that has its soma in the peripheral nervous system.
database_cross_reference: https://orcid.org/0000-0002-6095-8718

Axiom
annotated source: PNS neuron
annotated property: hasRelatedSynonym
annotated target: afferent neuron
database_cross_reference: FlyBase:FBrf0260546

larval CNS neuron
type: Class
equivalent class: Class
  intersection of: CNS neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuron
subclass of: CNS neuron
subclass of: Restriction
  on property: has soma location
  some values from: larval central nervous system
definition: Any neuron that has its soma in the late embryonic or larval central nervous system.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2023-11-09T16:11:09Z
database_cross_reference: VFB:FBbt_00059273
has exact synonym: embryonic/larval central nervous system neuron
has exact synonym: larval central nervous system neuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00059273
in subset: cur

Axiom
annotated source: larval CNS neuron
annotated property: definition
annotated target: Any neuron that has its soma in the late embryonic or larval central nervous system.
database_cross_reference: https://orcid.org/0000-0002-6095-8718

larval PNS neuron
type: Class
equivalent class: Class
  intersection of: PNS neuron
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: larval neuron
subclass of: PNS neuron
subclass of: Restriction
  on property: has soma location
  some values from: larval peripheral nervous system
definition: Any neuron that has its soma in the late embryonic or larval peripheral nervous system.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2023-11-09T16:12:15Z
database_cross_reference: VFB:FBbt_00059275
has exact synonym: embryonic/larval peripheral nervous system neuron
has exact synonym: larval peripheral nervous system neuron
has OBO namespace: fly_anatomy.ontology
id: FBbt:00059275
in subset: cur

Axiom
annotated source: larval PNS neuron
annotated property: definition
annotated target: Any neuron that has its soma in the late embryonic or larval peripheral nervous system.
database_cross_reference: https://orcid.org/0000-0002-6095-8718

glial cell of eye-antennal disc
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: overlaps
    some values from: eye-antennal disc
subclass of: larval glial cell
subclass of: Restriction
  on property: overlaps
  some values from: eye-antennal disc
definition: Any glial cell that is found in an eye-antennal disc (Gonzalez-Blas et al., 2020).
contributor: https://orcid.org/0000-0002-6095-8718
date: 2024-04-18T16:40:39Z
database_cross_reference: VFB:FBbt_00059299
has OBO namespace: fly_anatomy.ontology
id: FBbt:00059299

Axiom
annotated source: glial cell of eye-antennal disc
annotated property: definition
annotated target: Any glial cell that is found in an eye-antennal disc (Gonzalez-Blas et al., 2020).
database_cross_reference: FlyBase:FBrf0245749

somatic cell of ectoderm anlage
type: Class
equivalent class: Class
  intersection of: somatic cell
  intersection of: Restriction
    on property: part of
    some values from: ectoderm anlage
subclass of: somatic cell
subclass of: Restriction
  on property: part of
  some values from: ectoderm anlage
definition: A(n) somatic cell that is part of a(n) ectoderm anlage.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2024-04-24T15:19:10Z
has OBO namespace: fly_anatomy.ontology
id: FBbt:00059301

Axiom
annotated source: somatic cell of ectoderm anlage
annotated property: definition
annotated target: A(n) somatic cell that is part of a(n) ectoderm anlage.
database_cross_reference: FBC:Autogenerated

somatic cell of ectoderm
type: Class
equivalent class: Class
  intersection of: somatic cell
  intersection of: Restriction
    on property: part of
    some values from: ectoderm
subclass of: somatic cell
subclass of: Restriction
  on property: part of
  some values from: ectoderm
definition: A(n) somatic cell that is part of a(n) ectoderm.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2024-04-24T15:19:10Z
has exact synonym: ectodermal cell
has OBO namespace: fly_anatomy.ontology
id: FBbt:00059305

Axiom
annotated source: somatic cell of ectoderm
annotated property: definition
annotated target: A(n) somatic cell that is part of a(n) ectoderm.
database_cross_reference: FBC:Autogenerated

somatic cell of stage 5 embryo
type: Class
equivalent class: Class
  intersection of: somatic cell
  intersection of: Restriction
    on property: part of
    some values from: stage 5 embryo
subclass of: somatic cell
subclass of: Restriction
  on property: part of
  some values from: stage 5 embryo
definition: A(n) somatic cell that is part of a(n) stage 5 embryo.
contributor: https://orcid.org/0000-0002-6095-8718
date: 2024-04-24T15:19:10Z
has exact synonym: blastoderm cell
has OBO namespace: fly_anatomy.ontology
id: FBbt:00059313

Axiom
annotated source: somatic cell of stage 5 embryo
annotated property: definition
annotated target: A(n) somatic cell that is part of a(n) stage 5 embryo.
database_cross_reference: FBC:Autogenerated

cell body rind region
type: Class
subclass of: multi-cell-component structure
subclass of: Restriction
  on property: part of
  some values from: cell body rind of the central nervous system
definition: A subdivision of the cell body rind of the central nervous system. It includes the neuronal cell bodies.
contributor: Simon-Reeve-2162827703
date: 2010-09-08T02:26:08Z
database_cross_reference: VFB:FBbt_00100200
has exact synonym: cell body layer
has exact synonym: cortex region
has OBO namespace: fly_anatomy.ontology
id: FBbt:00100200
comment: Ito et al. (2014) may further subdivide cortex/rind regions into multiple facets. Subdivisions should be denoted by the addition of a single letter body-axis direction, e.g. rLHa for anterior to the lateral horn; rSMPm for medial to the superior medial protocerebrum, etc.

Axiom
annotated source: cell body rind region
annotated property: definition
annotated target: A subdivision of the cell body rind of the central nervous system. It includes the neuronal cell bodies.
database_cross_reference: FlyBase:FBrf0224194
database_cross_reference: https://orcid.org/0000-0002-7073-9172

Axiom
annotated source: cell body rind region
annotated property: hasExactSynonym
annotated target: cell body layer
database_cross_reference: FlyBase:FBrf0224194

glutamatergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0061535
subclass of: CL_0000679
subclass of: neuron
definition: Any neuron (FBbt:00005106) that is capable of some glutamate secretion, neurotransmission (GO:0061535).
contributor: Simon-Reeve-2162827703
date: 2010-10-13T02:35:30Z
database_cross_reference: CL:0000679
database_cross_reference: VFB:FBbt_00100291
has OBO namespace: fly_anatomy.ontology
id: FBbt:00100291
comment: Some glutamatergic neurons express ChAT transcripts (and reporters) at low levels, but do not produce functional enzyme (Lacin et al., 2019 - FBrf0242251).

Axiom
annotated source: glutamatergic neuron
annotated property: definition
annotated target: Any neuron (FBbt:00005106) that is capable of some glutamate secretion, neurotransmission (GO:0061535).
database_cross_reference: FBC:Autogenerated

multicellular structure
type: Class
subclass of: anatomical structure
definition: Anatomical structure that has multiple cells as parts.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2010-11-02T02:25:04Z
database_cross_reference: UBERON:0010000
has OBO namespace: fly_anatomy.ontology
id: FBbt:00100313

Axiom
annotated source: multicellular structure
annotated property: definition
annotated target: Anatomical structure that has multiple cells as parts.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

gut section
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part of
  some values from: gut
definition: A subdivision of the gut along its long axis.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2010-11-02T05:21:35Z
database_cross_reference: UBERON:0004921
has OBO namespace: fly_anatomy.ontology
id: FBbt:00100315

Axiom
annotated source: gut section
annotated property: definition
annotated target: A subdivision of the gut along its long axis.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

somatic cell
type: Class
subclass of: cell
contributor: https://orcid.org/0000-0002-7073-9172
date: 2010-11-04T08:35:02Z
has OBO namespace: fly_anatomy.ontology
id: FBbt:00100318

embryonic/larval alimentary canal
type: Class
subclass of: alimentary canal
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
definition: The entire embryonic/larval anatomical structure through which food and its digestion products are ingested, digested and excreted. At its anterior and posterior ends this includes structures that are not foregut or hindgut.
contributor: https://orcid.org/0000-0002-7073-9172
date: 2010-11-04T02:13:05Z
has OBO namespace: fly_anatomy.ontology
id: FBbt:00100323

Axiom
annotated source: embryonic/larval alimentary canal
annotated property: definition
annotated target: The entire embryonic/larval anatomical structure through which food and its digestion products are ingested, digested and excreted. At its anterior and posterior ends this includes structures that are not foregut or hindgut.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

lateral head epidermis
type: Class
subclass of: epidermis
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: embryonic dorsal pouch
subclass of: Restriction
  on property: develops from
  some values from: lateral head epidermis primordium
definition: .
has OBO namespace: fly_anatomy.ontology
id: FBbt:00105220
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: lateral head epidermis
annotated property: definition
annotated target: .
database_cross_reference: FBC:VH
database_cross_reference: https://orcid.org/0000-0002-7073-9172

late embryonic primordium of adult eye
type: Class
subclass of: embryonic primordium of adult eye
subclass of: Restriction
  on property: part of
  some values from: late embryo
subclass of: Restriction
  on property: develops from
  some values from: early embryonic primordium of adult eye
definition: Primordium of the late embryo that develops from the early primordium, and will give rise to the adult eye.
has exact synonym: adult eye primordium late
has OBO namespace: fly_anatomy.ontology
id: FBbt:00105515
in subset: cur

Axiom
annotated source: late embryonic primordium of adult eye
annotated property: definition
annotated target: Primordium of the late embryo that develops from the early primordium, and will give rise to the adult eye.
database_cross_reference: FBC:VH
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0151275
database_cross_reference: https://orcid.org/0000-0002-7073-9172

pedunculus of larval mushroom body
type: Class
subclass of: mushroom body pedunculus
subclass of: Restriction
  on property: part of
  some values from: embryonic/larval mushroom body
definition: Pedunculus of the larval mushroom body.
contributor: https://orcid.org/0000-0001-5948-3092
date: 2013-01-03T02:51:41Z
database_cross_reference: VFB:FBbt_00110187
database_cross_reference: larvalbrain_neuropil:393
database_cross_reference: larvalbrain_neuropil:571
has exact synonym: MB-P1
has exact synonym: larval peduncle
has narrow synonym: larval intermediate peduncle
has narrow synonym: larval intermediate pedunculus
has OBO namespace: fly_anatomy.ontology
id: FBbt:00110187
in subset: larval OF

Axiom
annotated source: pedunculus of larval mushroom body
annotated property: definition
annotated target: Pedunculus of the larval mushroom body.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

Axiom
annotated source: pedunculus of larval mushroom body
annotated property: hasExactSynonym
annotated target: MB-P1
database_cross_reference: FlyBase:FBrf0211533

Axiom
annotated source: pedunculus of larval mushroom body
annotated property: hasNarrowSynonym
annotated target: larval intermediate peduncle
database_cross_reference: FlyBase:FBrf0238440

medial lobe of larval mushroom body
type: Class
equivalent class: Class
  intersection of: mushroom body medial lobe
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: mushroom body medial lobe
subclass of: Restriction
  on property: part of
  some values from: lobe system of larval mushroom body
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: The medial lobe of the larval mushroom body. It is associated with appetitive memory (Eschbach et al., 2020).
contributor: https://orcid.org/0000-0001-5948-3092
date: 2013-01-03T02:51:41Z
database_cross_reference: VFB:FBbt_00110188
database_cross_reference: larvalbrain_neuropil:387
database_cross_reference: larvalbrain_neuropil:565
has exact synonym: horizontal lobe of larval mushroom body
has OBO namespace: fly_anatomy.ontology
id: FBbt:00110188
in subset: larval OF
comment: At third instar, the medial lobe comprise three types of Kenyon cells: embryonic-born gamma neurons, larval-born gamma neurons and larval born alpha'/beta' neurons (Pauls et al., 2010).

Axiom
annotated source: medial lobe of larval mushroom body
annotated property: definition
annotated target: The medial lobe of the larval mushroom body. It is associated with appetitive memory (Eschbach et al., 2020).
database_cross_reference: FlyBase:FBrf0211533
database_cross_reference: FlyBase:FBrf0245294

Axiom
annotated source: medial lobe of larval mushroom body
annotated property: hasExactSynonym
annotated target: horizontal lobe of larval mushroom body
database_cross_reference: FlyBase:FBrf0211016

vertical lobe of larval mushroom body
type: Class
equivalent class: Class
  intersection of: mushroom body vertical lobe
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: mushroom body vertical lobe
subclass of: Restriction
  on property: part of
  some values from: lobe system of larval mushroom body
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: The vertical lobe of the larval mushroom body (Pauls et al., 2010).
contributor: https://orcid.org/0000-0001-5948-3092
date: 2013-01-03T02:51:41Z
database_cross_reference: VFB:FBbt_00110189
database_cross_reference: larvalbrain_neuropil:421
database_cross_reference: larvalbrain_neuropil:599
has OBO namespace: fly_anatomy.ontology
id: FBbt:00110189
in subset: larval OF
comment: At third instar, the vertical lobe comprise three types of Kenyon cells: embryonic-born gamma neurons, larval-born gamma neurons and larval born alpha'/beta' neurons (Pauls et al., 2010).

Axiom
annotated source: vertical lobe of larval mushroom body
annotated property: definition
annotated target: The vertical lobe of the larval mushroom body (Pauls et al., 2010).
database_cross_reference: FlyBase:FBrf0211533

lobe system of larval mushroom body
type: Class
equivalent class: Class
  intersection of: lobe system of mushroom body
  intersection of: Restriction
    on property: overlaps
    some values from: larva
subclass of: lobe system of mushroom body
subclass of: Restriction
  on property: part of
  some values from: embryonic/larval mushroom body
subclass of: Restriction
  on property: overlaps
  some values from: larva
definition: The larval mushroom body lobe system consists of a dorsal branch and a medial branch (Pauls et al., 2010). At third instar, both lobes comprise three types of Kenyon cells: embryonic-born gamma neurons, larval-born gamma neurons and larval born alpha'/beta' neurons (Pauls et al., 2010).
contributor: https://orcid.org/0000-0001-5948-3092
date: 2013-10-09T16:48:14Z
database_cross_reference: VFB:FBbt_00110641
has OBO namespace: fly_anatomy.ontology
has related synonym: lobe of corpora pedunculata
has related synonym: lobe of mushroom body
id: FBbt:00110641
in subset: cur

Axiom
annotated source: lobe system of larval mushroom body
annotated property: definition
annotated target: The larval mushroom body lobe system consists of a dorsal branch and a medial branch (Pauls et al., 2010). At third instar, both lobes comprise three types of Kenyon cells: embryonic-born gamma neurons, larval-born gamma neurons and larval born alpha'/beta' neurons (Pauls et al., 2010).
database_cross_reference: FlyBase:FBrf0211533

cell body rind of larval brain
type: Class
subclass of: cell body rind region
subclass of: Restriction
  on property: part of
  some values from: larval brain
subclass of: Restriction
  on property: part of
  some values from: cell body rind of larval central nervous system
definition: Region of the larval cell body rind that overlies the neuropil of the brain.
contributor: https://orcid.org/0000-0001-5948-3092
date: 2015-10-29T11:43:24Z
database_cross_reference: VFB:FBbt_00111226
has exact synonym: cortex of larval brain
has OBO namespace: fly_anatomy.ontology
id: FBbt:00111226

Axiom
annotated source: cell body rind of larval brain
annotated property: definition
annotated target: Region of the larval cell body rind that overlies the neuropil of the brain.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

optic lobe neuroepithelial cell
type: Class
subclass of: stem cell
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: embryonic/larval optic lobe
subclass of: Restriction
  on property: develops from
  some values from: embryonic optic lobe primordium
definition: Symmetrically-dividing stem cell with epithelial properties and a columnar morphology that is a precursor to an optic neuroblast (Egger et al., 2007). These cells increase in number by symmetric divisions during embryonic and larval development (Egger et al., 2007). A small number differentiate into optic neuroblasts during the embryonic stage, while the remainder enter G0 quiescence prior to larval hatching (Hakes et al., 2018). Divisions resume in the first instar (Hakes et al., 2018), followed by differentiation to neuroblasts mainly during the third instar stage (Yasugi et al., 2008).
contributor: https://orcid.org/0000-0001-5948-3092
date: 2017-01-30T17:06:45Z
database_cross_reference: VFB:FBbt_00111738
has exact synonym: optic lobe NE cell
has OBO namespace: fly_anatomy.ontology
id: FBbt:00111738

Axiom
annotated source: optic lobe neuroepithelial cell
annotated property: definition
annotated target: Symmetrically-dividing stem cell with epithelial properties and a columnar morphology that is a precursor to an optic neuroblast (Egger et al., 2007). These cells increase in number by symmetric divisions during embryonic and larval development (Egger et al., 2007). A small number differentiate into optic neuroblasts during the embryonic stage, while the remainder enter G0 quiescence prior to larval hatching (Hakes et al., 2018). Divisions resume in the first instar (Hakes et al., 2018), followed by differentiation to neuroblasts mainly during the third instar stage (Yasugi et al., 2008).
database_cross_reference: FlyBase:FBrf0193624
database_cross_reference: FlyBase:FBrf0204205
database_cross_reference: FlyBase:FBrf0240123

Axiom
annotated source: optic lobe neuroepithelial cell
annotated property: hasExactSynonym
annotated target: optic lobe NE cell
database_cross_reference: FlyBase:FBrf0204205

anterior ectoderm anlage
type: Class
subclass of: developing embryonic structure
subclass of: anlage
subclass of: Restriction
  on property: part of
  some values from: ectoderm anlage
subclass of: Restriction
  on property: develops into
  some values from: anterior ectoderm
definition: Anlage that develops into the anterior ectoderm. It is found anterior to the dorsal, lateral and ventral regions of the ectoderm anlage and posterior to the anterior endoderm anlage at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
has OBO namespace: fly_anatomy.ontology
id: FBbt:01000119
in subset: cur

Axiom
annotated source: anterior ectoderm anlage
annotated property: definition
annotated target: Anlage that develops into the anterior ectoderm. It is found anterior to the dorsal, lateral and ventral regions of the ectoderm anlage and posterior to the anterior endoderm anlage at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
database_cross_reference: FlyBase:FBrf0244630

embryonic ventral trunk epidermis
type: Class
subclass of: ventral ectoderm derivative
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: embryonic ventral epidermis
subclass of: Restriction
  on property: develops from
  some values from: ventral trunk epidermis primordium
definition: The epidermis of the embryonic ventral trunk.
has OBO namespace: fly_anatomy.ontology
id: FBbt:01005747
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic ventral trunk epidermis
annotated property: definition
annotated target: The epidermis of the embryonic ventral trunk.
database_cross_reference: https://orcid.org/0000-0001-5948-3092

anatomical entity
type: Class
equivalent class: Class
  intersection of: CARO_0000000
  intersection of: Restriction
    on property: part of
    some values from: Drosophila melanogaster
subclass of: CARO_0000000
subclass of: Restriction
  on property: part of
  some values from: Drosophila melanogaster
definition: Anatomical entity which is part_of Drosophila melanogaster.
has alternative id: FBbt_root:00000000
database_cross_reference: UBERON:0001062
has OBO namespace: fly_anatomy.ontology
has related synonym: Drosophila
id: FBbt:10000000
in subset: EmbDevSlim
in subset: cur
in subset: larval OF

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: Anatomical entity which is part_of Drosophila melanogaster.
database_cross_reference: https://orcid.org/0000-0001-9114-8737

embryonic primordium of adult eye
type: Class
subclass of: embryonic imaginal tissue
subclass of: primordium
subclass of: anterior ectoderm derivative
subclass of: Restriction
  on property: develops from
  some values from: visual primordium
subclass of: Restriction
  on property: develops into
  some values from: eye disc
definition: Primordium of the embryo that will give rise to the adult eye. It corresponds to the most anterior region that develops from the visual primordium.
has exact synonym: P1 Eye
has exact synonym: adult eye primordium
has OBO namespace: fly_anatomy.ontology
id: FBbt:10005249
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: embryonic primordium of adult eye
annotated property: definition
annotated target: Primordium of the embryo that will give rise to the adult eye. It corresponds to the most anterior region that develops from the visual primordium.
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0151275

Axiom
annotated source: embryonic primordium of adult eye
annotated property: hasExactSynonym
annotated target: P1 Eye
database_cross_reference: https://orcid.org/0000-0002-7073-9172

denticle field anlage
type: Class
subclass of: developing embryonic structure
subclass of: anlage
subclass of: ventral ectoderm derivative
subclass of: Restriction
  on property: part of
  some values from: late extended germ band embryo
subclass of: Restriction
  on property: develops from
  some values from: ventral epidermis primordium
subclass of: Restriction
  on property: develops into
  some values from: denticle field primordium
definition: A(n) anlage that develops into some denticle field primordium. It develops from some ventral epidermis primordium.
has OBO namespace: fly_anatomy.ontology
has related synonym: A DenBl
id: FBbt:10005326
in subset: EmbDevSlim
in subset: cur

Axiom
annotated source: denticle field anlage
annotated property: definition
annotated target: A(n) anlage that develops into some denticle field primordium. It develops from some ventral epidermis primordium.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: denticle field anlage
annotated property: hasRelatedSynonym
annotated target: A DenBl
database_cross_reference: https://orcid.org/0000-0002-7073-9172

FlyBase CV
type: Class
definition: FlyBase miscellaneous controlled vocabulary term.
has OBO namespace: FlyBase miscellaneous CV
id: FBcv:0000000

descriptor
type: Class
subclass of: FlyBase CV
definition: Term that describes an allele, balancer, group or publication.
has OBO namespace: FlyBase miscellaneous CV
id: FBcv:0000013
in subset: do not annotate

Axiom
annotated source: descriptor
annotated property: definition
annotated target: Term that describes an allele, balancer, group or publication.
database_cross_reference: FBC:MMC

dataset descriptor
type: Class
subclass of: descriptor
definition: Term that describes a dataset.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: FlyBase miscellaneous CV
id: FBcv:0003021

Axiom
annotated source: dataset descriptor
annotated property: definition
annotated target: Term that describes a dataset.
database_cross_reference: FBC:GD

dataset entity type
type: Class
subclass of: dataset descriptor
definition: Term that specifies the dataset component type.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: dataset_entity_type
id: FBcv:0003022

Axiom
annotated source: dataset entity type
annotated property: definition
annotated target: Term that specifies the dataset component type.
database_cross_reference: FBC:GD

project
type: Class
subclass of: dataset entity type
definition: A set of biological data from a single study. Corresponds to the NCBI bioproject, GEO series or SRA study.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: dataset_entity_type
id: FBcv:0003023

Axiom
annotated source: project
annotated property: definition
annotated target: A set of biological data from a single study. Corresponds to the NCBI bioproject, GEO series or SRA study.
database_cross_reference: FBC:GD

biosample
type: Class
subclass of: dataset entity type
definition: Biological source material characterized by an experiment.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: dataset_entity_type
id: FBcv:0003024

Axiom
annotated source: biosample
annotated property: definition
annotated target: Biological source material characterized by an experiment.
database_cross_reference: FBC:GD

assay
type: Class
subclass of: dataset entity type
definition: Quantitative or qualitative assessment of biological source material to measure some attribute.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: dataset_entity_type
id: FBcv:0003025

Axiom
annotated source: assay
annotated property: definition
annotated target: Quantitative or qualitative assessment of biological source material to measure some attribute.
database_cross_reference: FBC:GD

dataset data type
type: Class
subclass of: dataset descriptor
definition: The data type content of a dataset.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: FlyBase miscellaneous CV
id: FBcv:0003028

Axiom
annotated source: dataset data type
annotated property: definition
annotated target: The data type content of a dataset.
database_cross_reference: FBC:GD

assay type
type: Class
subclass of: dataset data type
definition: The type of assay as characterized by its data content.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: assay_type
id: FBcv:0003050

Axiom
annotated source: assay type
annotated property: definition
annotated target: The type of assay as characterized by its data content.
database_cross_reference: FBC:GD

RNA-Seq
type: Class
subclass of: assay type
definition: A quantitative method for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
database_cross_reference: EFO:0008896
has OBO namespace: assay_type
id: FBcv:0003068

Axiom
annotated source: RNA-Seq
annotated property: definition
annotated target: A quantitative method for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing.
database_cross_reference: PMID:18451266

result type
type: Class
subclass of: dataset data type
definition: The type of result as characterized by its data content.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: result_type
id: FBcv:0003082

Axiom
annotated source: result type
annotated property: definition
annotated target: The type of result as characterized by its data content.
database_cross_reference: FBC:GD

analysis
type: Class
subclass of: result type
definition: A result that is produced from the detailed examination of data to come to some conclusion.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: result_type
id: FBcv:0003108

Axiom
annotated source: analysis
annotated property: definition
annotated target: A result that is produced from the detailed examination of data to come to some conclusion.
database_cross_reference: FBC:GD

dataset attribute
type: Class
subclass of: dataset descriptor
definition: A descriptor that describes some aspect of a dataset.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: FlyBase miscellaneous CV
id: FBcv:0003121

Axiom
annotated source: dataset attribute
annotated property: definition
annotated target: A descriptor that describes some aspect of a dataset.
database_cross_reference: FBC:GD

assay attribute
type: Class
subclass of: dataset attribute
definition: Some characteristic of an assay pertaining to the methods involved in processing the biological source material or generating the raw output data of the assay.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: assay_attribute
id: FBcv:0003175

Axiom
annotated source: assay attribute
annotated property: definition
annotated target: Some characteristic of an assay pertaining to the methods involved in processing the biological source material or generating the raw output data of the assay.
database_cross_reference: FBC:GD

assay method
type: Class
subclass of: assay attribute
definition: A method used to characterize the biological molecules isolated from a biosample.
contributor: http://orcid.org/0000-0001-5948-3092
date: 2016-02-24T19:19:21Z
has OBO namespace: assay_attribute
id: FBcv:0003208

Axiom
annotated source: assay method
annotated property: definition
annotated target: A method used to characterize the biological molecules isolated from a biosample.
database_cross_reference: FBC:GD

single-cell RNA-Seq
type: Class
subclass of: RNA-Seq
definition: A method for quantifying the transcriptome of individual cells, in which transcripts isolated from single cells are subjected to high-throughput sequencing and mapping to a reference genome.
contributor: http://orcid.org/0000-0002-6095-8718
date: 2021-07-26T12:18:07Z
database_cross_reference: EFO:0008913
database_cross_reference: OBI:0002631
has exact synonym: scRNA-Seq
has exact synonym: single-cell RNA sequencing assay
has OBO namespace: assay_type
id: FBcv:0009000

Axiom
annotated source: single-cell RNA-Seq
annotated property: definition
annotated target: A method for quantifying the transcriptome of individual cells, in which transcripts isolated from single cells are subjected to high-throughput sequencing and mapping to a reference genome.
database_cross_reference: PMID:28821273

Axiom
annotated source: single-cell RNA-Seq
annotated property: hasExactSynonym
annotated target: scRNA-Seq
database_cross_reference: PMID:32405060

cell clustering analysis
type: Class
subclass of: analysis
definition: A result that groups individual cells into populations sharing a similar transcriptional profile.
contributor: http://orcid.org/0000-0002-6095-8718
date: 2021-07-26T12:21:05Z
has OBO namespace: result_type
id: FBcv:0009002

Axiom
annotated source: cell clustering analysis
annotated property: definition
annotated target: A result that groups individual cells into populations sharing a similar transcriptional profile.
database_cross_reference: PMID:28821273

transcriptional cell cluster
type: Class
subclass of: result type
definition: A result that represents a population of cells sharing a similar transcriptional profile.
contributor: http://orcid.org/0000-0002-6095-8718
date: 2021-07-26T12:22:16Z
has OBO namespace: result_type
id: FBcv:0009003

Axiom
annotated source: transcriptional cell cluster
annotated property: definition
annotated target: A result that represents a population of cells sharing a similar transcriptional profile.
database_cross_reference: PMID:28821273

single-cell library sequencing
type: Class
subclass of: assay method
definition: A method to prepare and sequence a library of cDNAs obtained from single cells.
contributor: http://orcid.org/0000-0002-6095-8718
date: 2021-07-26T13:40:26Z
has OBO namespace: assay_attribute
id: FBcv:0009005

Axiom
annotated source: single-cell library sequencing
annotated property: definition
annotated target: A method to prepare and sequence a library of cDNAs obtained from single cells.
database_cross_reference: FBC:DPG

10x sequencing
type: Class
subclass of: single-cell library sequencing
definition: A method that uses the Chromium platform from 10x Genomics to prepare and sequence a cDNA library.
contributor: http://orcid.org/0000-0002-6095-8718
date: 2021-07-26T13:45:06Z
has OBO namespace: assay_attribute
id: FBcv:0009008

Axiom
annotated source: 10x sequencing
annotated property: definition
annotated target: A method that uses the Chromium platform from 10x Genomics to prepare and sequence a cDNA library.
database_cross_reference: PMID:29126257

Drosophila life
type: Class
subclass of: BFO_0000003
definition: The life of an individual of the species Drosophila melanogaster, from fertilization to death.
has alternative id: FBdv_root:00000000
has exact synonym: Drosophila life cycle
has OBO namespace: FlyBase_development_CV
id: FBdv:00000000

Axiom
annotated source: Drosophila life
annotated property: definition
annotated target: The life of an individual of the species Drosophila melanogaster, from fertilization to death.
database_cross_reference: FBC:DOS

cleavage stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: fertilized egg stage
definition: Stage during which the nucleus of the fertilized egg performs 13 rapid divisions, prior to cellularization (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997). The first seven divisions are synchronous (Campos-Ortega and Hartenstein, 1997). During the course of the subsequent three divisions, most of the nuclei approach the surface and then divide asynchronously a further three times, bringing the total number of cells to around 5000 (Campos-Ortega and Hartenstein, 1997). This corresponds to embryonic stages 1-4 (Hartenstein, 1993).
has OBO namespace: FlyBase_development_CV
id: FBdv:00000054
comment: Temporal ordering number - 25.

Axiom
annotated source: cleavage stage
annotated property: definition
annotated target: Stage during which the nucleus of the fertilized egg performs 13 rapid divisions, prior to cellularization (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997). The first seven divisions are synchronous (Campos-Ortega and Hartenstein, 1997). During the course of the subsequent three divisions, most of the nuclei approach the surface and then divide asynchronously a further three times, bringing the total number of cells to around 5000 (Campos-Ortega and Hartenstein, 1997). This corresponds to embryonic stages 1-4 (Hartenstein, 1993).
database_cross_reference: FlyBase:FBrf0064803
database_cross_reference: FlyBase:FBrf0089570

late extended germ band stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 10
subclass of: Restriction
  on property: immediately preceded by
  some values from: early extended germ band stage
definition: A collective term for stages 11 and 12.
has OBO namespace: FlyBase_development_CV
id: FBdv:00004450
comment: Temporal ordering number - 300.

Axiom
annotated source: late extended germ band stage
annotated property: definition
annotated target: A collective term for stages 11 and 12.
database_cross_reference: FBC:DOS

oogenesis
type: Class
subclass of: developmental process
definition: The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell.
database_cross_reference: GO:0048477
has exact synonym: oogenesis stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00004886
comment: Temporal ordering number - 10000.

Axiom
annotated source: oogenesis
annotated property: definition
annotated target: The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell.
database_cross_reference: GO:0048477

developmental stage
type: Class
subclass of: BFO_0000003
definition: A temporal subdivision of a developmental process.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2009-10-01T05:56:56Z
has alternative id: FBdv:00007010
has OBO namespace: FlyBase_development_CV
id: FBdv:00005259

Axiom
annotated source: developmental stage
annotated property: definition
annotated target: A temporal subdivision of a developmental process.
database_cross_reference: FBC:DOS

oogenesis stage S1
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
definition: Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005261
comment: Temporal ordering number - 10010.

Axiom
annotated source: oogenesis stage S1
annotated property: definition
annotated target: Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3).
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S2
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S1
definition: Oogenesis stage that begins when the cyst leaves the germarium (from this point the cyst is referred to as an egg chamber). During this stage, polyploidation of the nurse cells begins, they reach a ploidy of 8C, and follicle cells start to divide.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005262
comment: Temporal ordering number - 10020.

Axiom
annotated source: oogenesis stage S2
annotated property: definition
annotated target: Oogenesis stage that begins when the cyst leaves the germarium (from this point the cyst is referred to as an egg chamber). During this stage, polyploidation of the nurse cells begins, they reach a ploidy of 8C, and follicle cells start to divide.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S3
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S2
definition: Oogenesis stage that begins when the oocyte chromosomes condense into a karyosome attached to a distinctive spherical structure known as an endobody. The oocyte nucleolus disappears completely. During this stage, nurse cell ploidy reaches 16C.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005263
comment: Temporal ordering number - 10030.

Axiom
annotated source: oogenesis stage S3
annotated property: definition
annotated target: Oogenesis stage that begins when the oocyte chromosomes condense into a karyosome attached to a distinctive spherical structure known as an endobody. The oocyte nucleolus disappears completely. During this stage, nurse cell ploidy reaches 16C.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S4
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S3
definition: Oogenesis stage that begins when the nurse cells chromosomes become bulbous. Nurse cell chromosomes during this stage are polytene and reach a ploidy of 32C. The egg chamber is oval shaped.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005264
comment: Temporal ordering number - 10040.

Axiom
annotated source: oogenesis stage S4
annotated property: definition
annotated target: Oogenesis stage that begins when the nurse cells chromosomes become bulbous. Nurse cell chromosomes during this stage are polytene and reach a ploidy of 32C. The egg chamber is oval shaped.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S5
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S4
definition: Oogenesis stage that begins when nurse cell chromosomes are no longer bulbous - the association between homologs weakens so that these chromosomes no longer have a polytene structure. During this stage, posterior nurse cell nuclei have a higher ploidy (64C) than anterior ones.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005265
comment: Temporal ordering number - 10050.

Axiom
annotated source: oogenesis stage S5
annotated property: definition
annotated target: Oogenesis stage that begins when nurse cell chromosomes are no longer bulbous - the association between homologs weakens so that these chromosomes no longer have a polytene structure. During this stage, posterior nurse cell nuclei have a higher ploidy (64C) than anterior ones.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S6
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S5
definition: Oogenesis stage during which follicle cell division ceases.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005266
comment: Temporal ordering number - 10060.

Axiom
annotated source: oogenesis stage S6
annotated property: definition
annotated target: Oogenesis stage during which follicle cell division ceases.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S7
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S6
definition: Oogenesis stage during which polyploidation and enlargement of follicle cells begins. Nurse cell ploidy ranges from 256C (anterior) to 512C (posterior) and the egg chamber gains an elongated shape.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005267
comment: Temporal ordering number - 10070.

Axiom
annotated source: oogenesis stage S7
annotated property: definition
annotated target: Oogenesis stage during which polyploidation and enlargement of follicle cells begins. Nurse cell ploidy ranges from 256C (anterior) to 512C (posterior) and the egg chamber gains an elongated shape.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S8
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S7
definition: Oogenesis stage which begins when yolk first appears in the oocyte. Follicle cell migration over the oocyte begins during this stage (although mostly occurs during stage 9).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005268
comment: Temporal ordering number - 10080.

Axiom
annotated source: oogenesis stage S8
annotated property: definition
annotated target: Oogenesis stage which begins when yolk first appears in the oocyte. Follicle cell migration over the oocyte begins during this stage (although mostly occurs during stage 9).
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S9
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S8
definition: Oogenesis stage that begins when the border cells begin to migrate. During this stage: the oocyte is about 1/3 the length of the egg chamber with its nucleus located antero-dorsally; follicle cell migration results in an anterior to posterior gradient of follicle cell thickness with posterior cells being thicker (-> columnar) and posterior cells thinner ( -> squamous); border cell migration begins and ends; secretion of vitelline membrane begins.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005269
comment: Temporal ordering number - 10090.

Axiom
annotated source: oogenesis stage S9
annotated property: definition
annotated target: Oogenesis stage that begins when the border cells begin to migrate. During this stage: the oocyte is about 1/3 the length of the egg chamber with its nucleus located antero-dorsally; follicle cell migration results in an anterior to posterior gradient of follicle cell thickness with posterior cells being thicker (-> columnar) and posterior cells thinner ( -> squamous); border cell migration begins and ends; secretion of vitelline membrane begins.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S10
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S9
definition: Oogenesis stage that begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends with the beginning of nurse cell dumping.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005270
comment: Temporal ordering number - 10100.

Axiom
annotated source: oogenesis stage S10
annotated property: definition
annotated target: Oogenesis stage that begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends with the beginning of nurse cell dumping.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S10A
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S10
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S9
definition: Oogenesis stage which begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends when centripetal follicle migration begins. During this stage, the migrating border cells reach the oocyte. The oocyte is about 50% egg chamber length.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005271
comment: Temporal ordering number - 10110.

Axiom
annotated source: oogenesis stage S10A
annotated property: definition
annotated target: Oogenesis stage which begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends when centripetal follicle migration begins. During this stage, the migrating border cells reach the oocyte. The oocyte is about 50% egg chamber length.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074

oogenesis stage S10B
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S10
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S10A
definition: Oogenesis stage that begins when the centripetal follicle cells begin to migrate. As a result, the vitelline membrane extends into the opercular region. This stage ends when nurse cell dumping begins.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005272
comment: Temporal ordering number - 10120.

Axiom
annotated source: oogenesis stage S10B
annotated property: definition
annotated target: Oogenesis stage that begins when the centripetal follicle cells begin to migrate. As a result, the vitelline membrane extends into the opercular region. This stage ends when nurse cell dumping begins.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S11
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S10
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S10B
definition: Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins. The dorsal appendages begin to form during this stage. This stage ends when dying nurse cells form an anterior cap to the oocyte.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005273
comment: Temporal ordering number - 10130.

Axiom
annotated source: oogenesis stage S11
annotated property: definition
annotated target: Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins. The dorsal appendages begin to form during this stage. This stage ends when dying nurse cells form an anterior cap to the oocyte.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0043885
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S12
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S11
definition: Oogenesis stage that begins when dying nurse cells form an anterior cap to the oocyte. Shortly after this, nurse cell dumping and growth of the oocyte are complete. Elongation of the dorsal appendages and formation of the innermost chorionic layer and endochorion begins during this stage.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005274
comment: Temporal ordering number - 10160.

Axiom
annotated source: oogenesis stage S12
annotated property: definition
annotated target: Oogenesis stage that begins when dying nurse cells form an anterior cap to the oocyte. Shortly after this, nurse cell dumping and growth of the oocyte are complete. Elongation of the dorsal appendages and formation of the innermost chorionic layer and endochorion begins during this stage.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0043885
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S12A
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S12
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S11
definition: Innermost chorionic layer and endochorion begin to form in the anterior of the follicle.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005275
comment: Temporal ordering number - 10170.

Axiom
annotated source: oogenesis stage S12A
annotated property: definition
annotated target: Innermost chorionic layer and endochorion begin to form in the anterior of the follicle.
database_cross_reference: FlyBase:FBrf0043885

oogenesis stage S12B
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S12
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S12A
definition: Secretion of innermost chorionic layer and endochorion begins in the main follicle cells.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005276
comment: Temporal ordering number - 10180.

Axiom
annotated source: oogenesis stage S12B
annotated property: definition
annotated target: Secretion of innermost chorionic layer and endochorion begins in the main follicle cells.
database_cross_reference: FlyBase:FBrf0043885

oogenesis stage S12C
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S12
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S12B
definition: Formation of specialized endochorion structures in the anterior of the follicle: branches in the developing dorsal appendages; compact endochorion lacking the pillars seen in the rest of the follicle.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005277
comment: Temporal ordering number - 10190.

Axiom
annotated source: oogenesis stage S12C
annotated property: definition
annotated target: Formation of specialized endochorion structures in the anterior of the follicle: branches in the developing dorsal appendages; compact endochorion lacking the pillars seen in the rest of the follicle.
database_cross_reference: FlyBase:FBrf0021038

oogenesis stage S13
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S12
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S12C
definition: Oogenesis stage that begins when the micropyle begins to form. At the beginning of this stage, about 12-15 nurse cell nuclei remain at the anterior of the oocyte. By the end of this stage, none of these nuclei remain. Oocyte meiosis up to arrest at full metaphase I occurs during this stage.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005278
comment: Temporal ordering number - 10200.

Axiom
annotated source: oogenesis stage S13
annotated property: definition
annotated target: Oogenesis stage that begins when the micropyle begins to form. At the beginning of this stage, about 12-15 nurse cell nuclei remain at the anterior of the oocyte. By the end of this stage, none of these nuclei remain. Oocyte meiosis up to arrest at full metaphase I occurs during this stage.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0029744
database_cross_reference: FlyBase:FBrf0034074
database_cross_reference: FlyBase:FBrf0064777

oogenesis stage S13A
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S13
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S12C
definition: Oogenesis stage during which 12-15 nurse cell nuclei remain at the anterior of the oocyte. At this stage, the oocyte nucleus has reached its maximum volume and its chromosomes are compressed into a 5-7 micrometer karyosome.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005279
comment: Temporal ordering number - 10210. An alternative division of stage 13 into two sub-stages, A and B, has been defined on the basis of chorion development (see FBrf0043885). This ontology uses an alternative subdivision based on nurse cell nucleus number and oocyte meiosis, as the former at least, is easier to score than chorion ultrastructure.

Axiom
annotated source: oogenesis stage S13A
annotated property: definition
annotated target: Oogenesis stage during which 12-15 nurse cell nuclei remain at the anterior of the oocyte. At this stage, the oocyte nucleus has reached its maximum volume and its chromosomes are compressed into a 5-7 micrometer karyosome.
database_cross_reference: FlyBase:FBrf0029744

oogenesis stage S13B
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S13
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S13A
definition: Oogenesis stage during which 9-11 nurse cell nuclei remain at the anterior of the oocyte. During this stage, the nuclear membrane of the oocyte nucleus disappears, indicating the start of meiotic pro-metaphase.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005280
comment: Temporal ordering number - 10220. An alternative division of stage 13 into two sub-stages, A and B, has been defined on the basis of chorion development (see FBrf0043885). This ontology uses an alternative subdivision based on nurse cell nucleus number and oocyte meiosis, as the former at least, is easier to score than chorion ultrastructure.

Axiom
annotated source: oogenesis stage S13B
annotated property: definition
annotated target: Oogenesis stage during which 9-11 nurse cell nuclei remain at the anterior of the oocyte. During this stage, the nuclear membrane of the oocyte nucleus disappears, indicating the start of meiotic pro-metaphase.
database_cross_reference: FlyBase:FBrf0029744

oogenesis stage S13C
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S13
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S13B
definition: Oogenesis stage during which only 7-8 nurse cell nuclei remain at the anterior of the oocyte. At the beginning of this stage, oocyte chromosome bivalents separate from each other - indicating mid-prometaphase of oocyte meiosis.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005281
comment: Temporal ordering number - 10230.

Axiom
annotated source: oogenesis stage S13C
annotated property: definition
annotated target: Oogenesis stage during which only 7-8 nurse cell nuclei remain at the anterior of the oocyte. At the beginning of this stage, oocyte chromosome bivalents separate from each other - indicating mid-prometaphase of oocyte meiosis.
database_cross_reference: FlyBase:FBrf0029744

oogenesis stage S13D
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S13
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S13C
definition: Oogenesis stage during which only 5-6 nurse cell nuclei remain at the anterior of the oocyte. The oocyte nucleus is in late prometaphase:the bivalents arrange themselves in on the equatorial plane of the spindle; homologous centromeres are pulled towards the poles.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005282
comment: Temporal ordering number - 10240.

Axiom
annotated source: oogenesis stage S13D
annotated property: definition
annotated target: Oogenesis stage during which only 5-6 nurse cell nuclei remain at the anterior of the oocyte. The oocyte nucleus is in late prometaphase:the bivalents arrange themselves in on the equatorial plane of the spindle; homologous centromeres are pulled towards the poles.
database_cross_reference: FlyBase:FBrf0029744

oogenesis stage S14
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S13
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S13D
definition: The last stage of oogenesis. This stage begins when no nurse cell nuclei remain at the anterior of the egg (chamber). Exochorion formation and secretion occurs during this stage. The dorsal appendages complete their elongation and the follicle cells die.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005283
comment: Temporal ordering number - 10260.

Axiom
annotated source: oogenesis stage S14
annotated property: definition
annotated target: The last stage of oogenesis. This stage begins when no nurse cell nuclei remain at the anterior of the egg (chamber). Exochorion formation and secretion occurs during this stage. The dorsal appendages complete their elongation and the follicle cells die.
database_cross_reference: FlyBase:FBrf0043885

oogenesis stage S14A
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S14
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S13D
definition: Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005284
comment: Temporal ordering number - 10270.

Axiom
annotated source: oogenesis stage S14A
annotated property: definition
annotated target: Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0043885

oogenesis stage S14B
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: oogenesis stage S14
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S14A
definition: Secretion of the exochorion begins and ends.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005285
comment: Temporal ordering number - 10280.

Axiom
annotated source: oogenesis stage S14B
annotated property: definition
annotated target: Secretion of the exochorion begins and ends.
database_cross_reference: FlyBase:FBrf0021038
database_cross_reference: FlyBase:FBrf0043885

egg stage
type: Class
subclass of: developmental stage
definition: The stage of the Drosophila life-cycle from maturation of an egg to the end of fertilization. At the beginning of this stage, the nucleus is arrested in meiotic metaphase I. The completion of meiosis and the start of protein synthesis are triggered by ovulation. If the female has already mated, fertilization begins during meiosis.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005286
comment: Temporal ordering number - 10290.

Axiom
annotated source: egg stage
annotated property: definition
annotated target: The stage of the Drosophila life-cycle from maturation of an egg to the end of fertilization. At the beginning of this stage, the nucleus is arrested in meiotic metaphase I. The completion of meiosis and the start of protein synthesis are triggered by ovulation. If the female has already mated, fertilization begins during meiosis.
database_cross_reference: FlyBase:FBrf0064779

unfertilized egg stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: egg stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S14
subclass of: Restriction
  on property: immediately preceded by
  some values from: oogenesis stage S14B
definition: Developmental stage that starts with ovulation, at the end of oogenesis, until the egg is fertilized by a sperm.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005287
comment: Temporal ordering number - 10300.

Axiom
annotated source: unfertilized egg stage
annotated property: definition
annotated target: Developmental stage that starts with ovulation, at the end of oogenesis, until the egg is fertilized by a sperm.
database_cross_reference: FlyBase:FBrf0158848

fertilized egg stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: egg stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: unfertilized egg stage
definition: Developmental stage that starts with sperm entry until the first mitotic division of the zygote.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005288
comment: Temporal ordering number - 10.

Axiom
annotated source: fertilized egg stage
annotated property: definition
annotated target: Developmental stage that starts with sperm entry until the first mitotic division of the zygote.
database_cross_reference: FlyBase:FBrf0229233

embryonic stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: unfertilized egg stage
subclass of: Restriction
  on property: immediately precedes
  some values from: larval stage
subclass of: Restriction
  on property: immediately precedes
  some values from: first instar larval stage
definition: Life stage that begins with a fertilized egg, and finishes with hatching at the end of embryonic stage 17 (Campos-Ortega and Hartenstein, 1997).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005289
comment: Temporal ordering number - 20.

Axiom
annotated source: embryonic stage
annotated property: definition
annotated target: Life stage that begins with a fertilized egg, and finishes with hatching at the end of embryonic stage 17 (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0089570

pre-blastoderm stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: cleavage stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: fertilized egg stage
definition: Stage prior to the formation of the syncitial blastoderm, including the first 9 cell divisions and the migration of nuclei to the periphery (cortex) of the embryo (Foe and Alberts, 1983; Jaeger et al., 2012). This lasts from fertilization to embryonic stage 3 (Campos-Ortega and Hartenstein, 1997).
has exact synonym: pre-blastoderm
has OBO namespace: FlyBase_development_CV
id: FBdv:00005290
comment: Temporal ordering number - 30.

Axiom
annotated source: pre-blastoderm stage
annotated property: definition
annotated target: Stage prior to the formation of the syncitial blastoderm, including the first 9 cell divisions and the migration of nuclei to the periphery (cortex) of the embryo (Foe and Alberts, 1983; Jaeger et al., 2012). This lasts from fertilization to embryonic stage 3 (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0039741
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0220623

embryonic stage 1
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pre-blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: fertilized egg stage
definition: The embryonic stage that lasts from the end of fertilization to the end of the second nuclear division. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005291
comment: Temporal ordering number - 40.

Axiom
annotated source: embryonic stage 1
annotated property: definition
annotated target: The embryonic stage that lasts from the end of fertilization to the end of the second nuclear division. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0064779
database_cross_reference: FlyBase:FBrf0089570

embryonic cycle 1
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 1
subclass of: Restriction
  on property: immediately preceded by
  some values from: fertilized egg stage
definition: The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005292
comment: Temporal ordering number - 50.

Axiom
annotated source: embryonic cycle 1
annotated property: definition
annotated target: The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

embryonic stage 2
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pre-blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 1
definition: Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005293
comment: Temporal ordering number - 70.

Axiom
annotated source: embryonic stage 2
annotated property: definition
annotated target: Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL).
database_cross_reference: FlyBase:FBrf0089570

embryonic cycle 2
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 1
definition: The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005294
comment: Temporal ordering number - 60.

Axiom
annotated source: embryonic cycle 2
annotated property: definition
annotated target: The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

embryonic cycle 3
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 1
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 2
definition: The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005295
comment: Temporal ordering number - 80.

Axiom
annotated source: embryonic cycle 3
annotated property: definition
annotated target: The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

embryonic cycle 4
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 3
definition: The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005296
comment: Temporal ordering number - 90.

Axiom
annotated source: embryonic cycle 4
annotated property: definition
annotated target: The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

embryonic cycle 5
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 4
definition: The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005297
comment: Temporal ordering number - 100.

Axiom
annotated source: embryonic cycle 5
annotated property: definition
annotated target: The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

embryonic cycle 6
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 5
definition: The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005298
comment: Temporal ordering number - 110.

Axiom
annotated source: embryonic cycle 6
annotated property: definition
annotated target: The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

embryonic cycle 7
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 6
definition: The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005299
comment: Temporal ordering number - 120.

Axiom
annotated source: embryonic cycle 7
annotated property: definition
annotated target: The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

embryonic cycle 8
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 7
definition: The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005300
comment: Temporal ordering number - 130.

Axiom
annotated source: embryonic cycle 8
annotated property: definition
annotated target: The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

embryonic stage 3
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pre-blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 8
definition: Nuclear division 9. The cleavage nuclei complete their migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005301
comment: Temporal ordering number - 140.

Axiom
annotated source: embryonic stage 3
annotated property: definition
annotated target: Nuclear division 9. The cleavage nuclei complete their migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic cycle 9
type: Class
subclass of: embryonic cycle
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 3
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 2
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 8
definition: The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005302
comment: Temporal ordering number - 150.

Axiom
annotated source: embryonic cycle 9
annotated property: definition
annotated target: The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
database_cross_reference: FlyBase:FBrf0049535

blastoderm stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pre-blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 3
definition: Stage during which most of the nuclei are arranged as a monolayer at the cortex (periphery) of the embryo (Foe and Alberts, 1983; Jaeger et al., 2012). It begins shortly after completion of the ninth cleavage division and lasts until the onset of gastrulation, including cleavage cycles 10-14A (Foe and Alberts, 1983; Jaeger et al., 2012). This corresponds to embryonic stages 4 (syncitial blastoderm stage) and 5 (cellular blastoderm stage) (Campos-Ortega and Hartenstein, 1997).
has exact synonym: blastoderm
has OBO namespace: FlyBase_development_CV
id: FBdv:00005304
comment: Temporal ordering number - 160.

Axiom
annotated source: blastoderm stage
annotated property: definition
annotated target: Stage during which most of the nuclei are arranged as a monolayer at the cortex (periphery) of the embryo (Foe and Alberts, 1983; Jaeger et al., 2012). It begins shortly after completion of the ninth cleavage division and lasts until the onset of gastrulation, including cleavage cycles 10-14A (Foe and Alberts, 1983; Jaeger et al., 2012). This corresponds to embryonic stages 4 (syncitial blastoderm stage) and 5 (cellular blastoderm stage) (Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0039741
database_cross_reference: FlyBase:FBrf0089570
database_cross_reference: FlyBase:FBrf0220623

embryonic stage 4
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pre-blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 3
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic cycle 9
definition: Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying).
has exact synonym: syncytial blastoderm stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005306
comment: Temporal ordering number - 170.

Axiom
annotated source: embryonic stage 4
annotated property: definition
annotated target: Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

Axiom
annotated source: embryonic stage 4
annotated property: hasExactSynonym
annotated target: syncytial blastoderm stage
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 5
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: cleavage stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 4
definition: Cellularization. Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees: approximately 40 minutes (130-170 minutes after egg laying).
has exact synonym: cellular blastoderm stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005311
comment: Temporal ordering number - 210.

Axiom
annotated source: embryonic stage 5
annotated property: definition
annotated target: Cellularization. Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees: approximately 40 minutes (130-170 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

Axiom
annotated source: embryonic stage 5
annotated property: hasExactSynonym
annotated target: cellular blastoderm stage
database_cross_reference: FlyBase:FBrf0089570

gastrula stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 5
definition: Stage during which gastrulation occurs. During this stage, cells from the polar caps and the mid-ventral part of the blastoderm invaginate and ultimately generate the germ layers (Hartenstein, 1993). This encompasses embryonic stages 6-8 (Hartenstein, 1993).
has exact synonym: gastrula
has exact synonym: gastrulation stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005317
comment: Temporal ordering number - 220.

Axiom
annotated source: gastrula stage
annotated property: definition
annotated target: Stage during which gastrulation occurs. During this stage, cells from the polar caps and the mid-ventral part of the blastoderm invaginate and ultimately generate the germ layers (Hartenstein, 1993). This encompasses embryonic stages 6-8 (Hartenstein, 1993).
database_cross_reference: FlyBase:FBrf0064803

embryonic stage 6
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: gastrula stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: blastoderm stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 5
definition: Stage 6 begins when the ventral furrow becomes apparent, an event which is followed rapidly by the formation of the cephalic furrow. Stage 6 ends when the pole cells have adopted a dorsal (horizontal) position at the posterior. Duration at 25 degrees C: approximately 10 minutes (170-180 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005318
comment: Temporal ordering number - 230.

Axiom
annotated source: embryonic stage 6
annotated property: definition
annotated target: Stage 6 begins when the ventral furrow becomes apparent, an event which is followed rapidly by the formation of the cephalic furrow. Stage 6 ends when the pole cells have adopted a dorsal (horizontal) position at the posterior. Duration at 25 degrees C: approximately 10 minutes (170-180 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 7
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: gastrula stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 6
definition: Stage 7 begins when the pole cells have adopted a dorsal (horizontal) position at the posterior. Invagination of the anterior and posterior midgut and hindgut follows. The 'discoid plate' that carries the pole cells forms a pocket. Transverse furrows (dorsal folds) form on the dorsal surface. This stage ends when the anterior wall of the amnioproctodeal invagination starts moving anteriorly and the pole cells are no longer visible externally. Duration at 25 degrees C: approximately 10 minutes (180-190 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005319
comment: Temporal ordering number - 240.

Axiom
annotated source: embryonic stage 7
annotated property: definition
annotated target: Stage 7 begins when the pole cells have adopted a dorsal (horizontal) position at the posterior. Invagination of the anterior and posterior midgut and hindgut follows. The 'discoid plate' that carries the pole cells forms a pocket. Transverse furrows (dorsal folds) form on the dorsal surface. This stage ends when the anterior wall of the amnioproctodeal invagination starts moving anteriorly and the pole cells are no longer visible externally. Duration at 25 degrees C: approximately 10 minutes (180-190 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

extended germ band stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: gastrula stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 8
definition: Stages during which the germ band is extended - 9-12.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005321
comment: Temporal ordering number - 260.

Axiom
annotated source: extended germ band stage
annotated property: definition
annotated target: Stages during which the germ band is extended - 9-12.
database_cross_reference: FBC:DOS
database_cross_reference: FlyBase:FBrf0229323

embryonic stage 8
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: gastrula stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 7
definition: Stage 8 starts with the rapid phase of germ band extension and ends with the beginning of mesodermal segmentation. By the end of this stage germ band extension has progressed to the point where the proctodeal opening is at about 60% egg length and the dorsal folds (transverse furrows) are no longer visible. Duration at 25 degrees C: approximately 30 minutes (190-220 minutes after egg laying).
has exact synonym: rapidly extending germ band stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005322
comment: Temporal ordering number - 250.

Axiom
annotated source: embryonic stage 8
annotated property: definition
annotated target: Stage 8 starts with the rapid phase of germ band extension and ends with the beginning of mesodermal segmentation. By the end of this stage germ band extension has progressed to the point where the proctodeal opening is at about 60% egg length and the dorsal folds (transverse furrows) are no longer visible. Duration at 25 degrees C: approximately 30 minutes (190-220 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 9
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: early extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: gastrula stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 8
definition: Stage 9 begins when mesodermal segmentation becomes (transiently) visible, and ends with the appearance of the stomodeal invagination slightly ventral to the anterior pole. Duration at 25 degrees C: approximately 40 minutes (220-260 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005323
comment: Temporal ordering number - 280.

Axiom
annotated source: embryonic stage 9
annotated property: definition
annotated target: Stage 9 begins when mesodermal segmentation becomes (transiently) visible, and ends with the appearance of the stomodeal invagination slightly ventral to the anterior pole. Duration at 25 degrees C: approximately 40 minutes (220-260 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 10
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: early extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 9
definition: Stage 10 begins with the appearance of the stomodeal invagination, slightly ventral to the anterior pole. Periodic furrows appear in the embryonic epidermis around the middle of the stage. The germ band continues to extend, reaching its maximum extent of 75% egg length towards the end of the stage. The end of the stage is marked by the beginning of invagination of the tracheal placodes. Duration at 25 degrees : approximately 60 minutes (260-320 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005324
comment: Temporal ordering number - 290.

Axiom
annotated source: embryonic stage 10
annotated property: definition
annotated target: Stage 10 begins with the appearance of the stomodeal invagination, slightly ventral to the anterior pole. Periodic furrows appear in the embryonic epidermis around the middle of the stage. The germ band continues to extend, reaching its maximum extent of 75% egg length towards the end of the stage. The end of the stage is marked by the beginning of invagination of the tracheal placodes. Duration at 25 degrees : approximately 60 minutes (260-320 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 11
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: late extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 10
subclass of: Restriction
  on property: immediately preceded by
  some values from: early extended germ band stage
definition: Stage 11 begins with the invagination of the tracheal placodes. Para-segmental furrow form and segment boundary furrows become deep folds. Within the head, gnathal protuberances become apparent. The end of this stage is signaled by the appearance of a distinct cleft at the posterior pole of the embryo, which becomes detached from the vitelline membrane. This marks the beginning of germ-band retraction. Duration at 25 degrees C: approximately 120 minutes (320-440 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005325
comment: Temporal ordering number - 310.

Axiom
annotated source: embryonic stage 11
annotated property: definition
annotated target: Stage 11 begins with the invagination of the tracheal placodes. Para-segmental furrow form and segment boundary furrows become deep folds. Within the head, gnathal protuberances become apparent. The end of this stage is signaled by the appearance of a distinct cleft at the posterior pole of the embryo, which becomes detached from the vitelline membrane. This marks the beginning of germ-band retraction. Duration at 25 degrees C: approximately 120 minutes (320-440 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 12
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: late extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 11
definition: Germ band retraction. Stage 12 begins when germ-band retraction starts and ends when this process is complete so that the prospective anal plate occupies the posterior pole. During this stage the posterior and anterior midgut primordia meet and fuse and the tracheal pits fuse to form the tracheal tree. Duration at 25 degrees C: approximately 120 minutes (440-560 minutes after egg laying).
has exact synonym: retracting germ band stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005327
comment: Temporal ordering number - 320.

Axiom
annotated source: embryonic stage 12
annotated property: definition
annotated target: Germ band retraction. Stage 12 begins when germ-band retraction starts and ends when this process is complete so that the prospective anal plate occupies the posterior pole. During this stage the posterior and anterior midgut primordia meet and fuse and the tracheal pits fuse to form the tracheal tree. Duration at 25 degrees C: approximately 120 minutes (440-560 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 13
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: dorsal closure stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: late extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 12
definition: Stage 13 begins at the completion of germ-band retraction, when the prospective anal plate occupy the posterior pole. The dorsal ridge becomes apparent externally; the clypeolabrum retracts, leaving a triangular shaped gap at the anterior pole; the labium moves to the ventral midline. This stage ends when head involution begins. Duration at 25 degrees C: Approximately 60 minutes (560-620 minutes after egg laying).
has exact synonym: contracted germ band stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005328
comment: Temporal ordering number - 340.

Axiom
annotated source: embryonic stage 13
annotated property: definition
annotated target: Stage 13 begins at the completion of germ-band retraction, when the prospective anal plate occupy the posterior pole. The dorsal ridge becomes apparent externally; the clypeolabrum retracts, leaving a triangular shaped gap at the anterior pole; the labium moves to the ventral midline. This stage ends when head involution begins. Duration at 25 degrees C: Approximately 60 minutes (560-620 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 14
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: dorsal closure stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 13
definition: Stage 14 begins with the initiation of head involution. Closure of the midgut around the yolk and dorsal closure continue. Dorsal closure is 80% complete by the end of this stage. This stage ends with the appearance of the second midgut constriction. Duration at 25 degrees C: approximately 60 minutes (620-680 minutes after egg laying).
has exact synonym: head involution stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005330
comment: Temporal ordering number - 350.

Axiom
annotated source: embryonic stage 14
annotated property: definition
annotated target: Stage 14 begins with the initiation of head involution. Closure of the midgut around the yolk and dorsal closure continue. Dorsal closure is 80% complete by the end of this stage. This stage ends with the appearance of the second midgut constriction. Duration at 25 degrees C: approximately 60 minutes (620-680 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

dorsal closure stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: late extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 12
definition: Stage following germ band retraction, during which dorsal closure happens (Hartenstein, 1993). Dorsal closure occurs by extension of the dorsal epidermal primordium on either side, leading to fusion at the dorsal midline (Campos-Ortega and Hartenstein, 1997). This corresponds to embryonic stages 13-15 (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005331
comment: Temporal ordering number - 330.

Axiom
annotated source: dorsal closure stage
annotated property: definition
annotated target: Stage following germ band retraction, during which dorsal closure happens (Hartenstein, 1993). Dorsal closure occurs by extension of the dorsal epidermal primordium on either side, leading to fusion at the dorsal midline (Campos-Ortega and Hartenstein, 1997). This corresponds to embryonic stages 13-15 (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997).
database_cross_reference: FlyBase:FBrf0064803
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 15
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: dorsal closure stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 14
definition: Stage 15 begins with the appearance of the second midgut constriction. During this stage the 1st and 3rd midgut constrictions form, dorsal closure is completed, and epidermal segmentation is accomplished. This stage ends when the intersegmental grooves can be distinguished at mid-dorsal level. Duration at 25 degrees C: approximately 100 minutes (680-780 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005332
comment: Temporal ordering number - 360.

Axiom
annotated source: embryonic stage 15
annotated property: definition
annotated target: Stage 15 begins with the appearance of the second midgut constriction. During this stage the 1st and 3rd midgut constrictions form, dorsal closure is completed, and epidermal segmentation is accomplished. This stage ends when the intersegmental grooves can be distinguished at mid-dorsal level. Duration at 25 degrees C: approximately 100 minutes (680-780 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

late embryonic stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: dorsal closure stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 15
definition: Embryonic stages 16-17.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005333
comment: Temporal ordering number - 370.

Axiom
annotated source: late embryonic stage
annotated property: definition
annotated target: Embryonic stages 16-17.
database_cross_reference: FBC:DOS

embryonic stage 16
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: late embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: dorsal closure stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 15
definition: Stage 16 begins when the intersegmental grooves can be distinguished at mid-dorsal level, and ends when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. During this stage the ventral cord retracts to about 60% egg length. Duration at 25 degrees C: approximately 180 minutes (780-960 minutes after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005334
comment: Temporal ordering number - 380.

Axiom
annotated source: embryonic stage 16
annotated property: definition
annotated target: Stage 16 begins when the intersegmental grooves can be distinguished at mid-dorsal level, and ends when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. During this stage the ventral cord retracts to about 60% egg length. Duration at 25 degrees C: approximately 180 minutes (780-960 minutes after egg laying).
database_cross_reference: FlyBase:FBrf0089570

embryonic stage 17
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: late embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 16
definition: Stage 17 begins when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. It lasts until hatching of the embryo (approximately 24 hours after egg laying), during which time much terminal differentiation occurs, the tracheal tree fills with air, so becoming completely visible, and the ventral cord continues to retract. Duration at 25 degrees C: approximately 8 hours (16-24 hours after egg laying).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005335
comment: Temporal ordering number - 390.

Axiom
annotated source: embryonic stage 17
annotated property: definition
annotated target: Stage 17 begins when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. It lasts until hatching of the embryo (approximately 24 hours after egg laying), during which time much terminal differentiation occurs, the tracheal tree fills with air, so becoming completely visible, and the ventral cord continues to retract. Duration at 25 degrees C: approximately 8 hours (16-24 hours after egg laying).
database_cross_reference: FlyBase:FBrf0089570

larval stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 17
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 17(iv)
subclass of: Restriction
  on property: immediately precedes
  some values from: prepupal stage
subclass of: Restriction
  on property: immediately precedes
  some values from: P-stage
definition: The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005336
comment: Temporal ordering number - 400.

Axiom
annotated source: larval stage
annotated property: definition
annotated target: The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation.
database_cross_reference: FBC:DOS

first instar larval stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: substage of
  some values from: larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: late embryonic stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 17
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 17(iv)
subclass of: Restriction
  on property: immediately precedes
  some values from: second instar larval stage
definition: The first larval instar begins at hatching and ends at the first larval molt. Anterior spiracles are not yet present; posterior spiracles have two openings each. Salivary glands are very small and all cells are uniform in size. Mouth hooks typically have one tooth. Duration at 25 degrees C: approximately 25 hours (24-49 hours after egg laying; 0-25 hours after hatching).
database_cross_reference: UBERON:8000000
has exact synonym: L1
has exact synonym: first instar larva
has OBO namespace: FlyBase_development_CV
id: FBdv:00005337
comment: Temporal ordering number - 410.

Axiom
annotated source: first instar larval stage
annotated property: definition
annotated target: The first larval instar begins at hatching and ends at the first larval molt. Anterior spiracles are not yet present; posterior spiracles have two openings each. Salivary glands are very small and all cells are uniform in size. Mouth hooks typically have one tooth. Duration at 25 degrees C: approximately 25 hours (24-49 hours after egg laying; 0-25 hours after hatching).
database_cross_reference: FlyBase:FBrf0007733

second instar larval stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: substage of
  some values from: larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: first instar larval stage
subclass of: Restriction
  on property: immediately precedes
  some values from: third instar larval stage
definition: The second larval instar begins at the first larval molt and ends at the second larval molt. Larvae are actively feeding and crawling in the food. Distinct anterior spiracles are present as enlargements at the end of the tracheal trunk, but not open to the outside; posterior spiracles have three openings each, and four groups of small unbranched hairs. The salivary glands extend to the first abdominal segment, and have cells that are uniform in size. Mouth hooks typically have two or three teeth. Duration at 25 degrees C: approximately 23 hours (49-72 hours after egg laying; 25-48 hours after hatching).
database_cross_reference: UBERON:8000001
has exact synonym: L2
has exact synonym: second instar larva
has OBO namespace: FlyBase_development_CV
id: FBdv:00005338
comment: Temporal ordering number - 420.

Axiom
annotated source: second instar larval stage
annotated property: definition
annotated target: The second larval instar begins at the first larval molt and ends at the second larval molt. Larvae are actively feeding and crawling in the food. Distinct anterior spiracles are present as enlargements at the end of the tracheal trunk, but not open to the outside; posterior spiracles have three openings each, and four groups of small unbranched hairs. The salivary glands extend to the first abdominal segment, and have cells that are uniform in size. Mouth hooks typically have two or three teeth. Duration at 25 degrees C: approximately 23 hours (49-72 hours after egg laying; 25-48 hours after hatching).
database_cross_reference: FlyBase:FBrf0007733

third instar larval stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: substage of
  some values from: larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: second instar larval stage
subclass of: Restriction
  on property: immediately precedes
  some values from: prepupal stage
subclass of: Restriction
  on property: immediately precedes
  some values from: P-stage
definition: The third larval instar begins at the second larval molt and ends at puparium formation. Anterior spiracles are open to the outside; posterior spiracles have three openings each, and four groups of large branched hairs. The salivary glands extend to the second abdominal segment, with cells larger in the posterior than in the anterior of the gland. Mouth hooks typically have 9-12 teeth. About 24 hours before pupariation (at 25 degree C), larvae stop feeding and climb away from their food. Duration at 25 degrees C: approximately 48 hours (72-120 hours after egg laying; 48-96 hours after hatching).
database_cross_reference: UBERON:8000002
has exact synonym: L3
has OBO namespace: FlyBase_development_CV
has related synonym: third instar larva
id: FBdv:00005339
comment: Temporal ordering number - 430.

Axiom
annotated source: third instar larval stage
annotated property: definition
annotated target: The third larval instar begins at the second larval molt and ends at puparium formation. Anterior spiracles are open to the outside; posterior spiracles have three openings each, and four groups of large branched hairs. The salivary glands extend to the second abdominal segment, with cells larger in the posterior than in the anterior of the gland. Mouth hooks typically have 9-12 teeth. About 24 hours before pupariation (at 25 degree C), larvae stop feeding and climb away from their food. Duration at 25 degrees C: approximately 48 hours (72-120 hours after egg laying; 48-96 hours after hatching).
database_cross_reference: FlyBase:FBrf0007733

early third instar larval stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: second instar larval stage
definition: Third instar larva prior to the wandering stage (approximately the first 24 hours of the third instar larval stage under standard conditions at 25'C.).
contributor: http://orcid.org/0000-0002-7073-9172
date: 2008-11-13T11:51:56Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00005340
comment: Temporal ordering number - 440.

Axiom
annotated source: early third instar larval stage
annotated property: definition
annotated target: Third instar larva prior to the wandering stage (approximately the first 24 hours of the third instar larval stage under standard conditions at 25'C.).
database_cross_reference: FlyBase:FBrf0049147

wandering third instar larval stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: late third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: early third instar larval stage
definition: Stage of the third larval instar during which the larva wanders out of the food and climbs. Under optimum conditions at 25'C, this occurs approximately 24 hours after the start of the third instar larval stage.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2008-11-13T11:55:46Z
has broad synonym: late third instar
has broad synonym: post-feeding larva
has OBO namespace: FlyBase_development_CV
id: FBdv:00005341
comment: Temporal ordering number - 460.

Axiom
annotated source: wandering third instar larval stage
annotated property: definition
annotated target: Stage of the third larval instar during which the larva wanders out of the food and climbs. Under optimum conditions at 25'C, this occurs approximately 24 hours after the start of the third instar larval stage.
database_cross_reference: FlyBase:FBrf0049147

prepupal stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: substage of
  some values from: P-stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar larval stage L2
subclass of: Restriction
  on property: immediately preceded by
  some values from: late third instar larval stage
subclass of: Restriction
  on property: immediately precedes
  some values from: pupal stage
definition: The prepupal stage begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C: approximately 12 hours. (120-132.2 hours after egg laying; 0-12.2 hours after puparium formation).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005342
comment: Temporal ordering number - 500.

Axiom
annotated source: prepupal stage
annotated property: definition
annotated target: The prepupal stage begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C: approximately 12 hours. (120-132.2 hours after egg laying; 0-12.2 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

prepupal stage P1
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: prepupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar larval stage L2
subclass of: Restriction
  on property: immediately preceded by
  some values from: late third instar larval stage
definition: Extends from puparium formation through tanning of the pupal cuticle. Posterior spiracles and ridge between anterior spiracles tan orange. Wriggling stops completely. Puparium becomes brown to the unaided eye. Duration at 25 degrees C: approximately 20 minutes. (120-120.3 hours after egg laying; 0-0.3 hours after puparium formation).
has exact synonym: pupal stage P1
has exact synonym: puparium formation
has exact synonym: white puparium stage
has narrow synonym: pupal stage P0
has narrow synonym: white prepupa
has OBO namespace: FlyBase_development_CV
id: FBdv:00005343
comment: Temporal ordering number - 510.

Axiom
annotated source: prepupal stage P1
annotated property: definition
annotated target: Extends from puparium formation through tanning of the pupal cuticle. Posterior spiracles and ridge between anterior spiracles tan orange. Wriggling stops completely. Puparium becomes brown to the unaided eye. Duration at 25 degrees C: approximately 20 minutes. (120-120.3 hours after egg laying; 0-0.3 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: prepupal stage P1
annotated property: hasExactSynonym
annotated target: puparium formation
database_cross_reference: FlyBase:FBrf0036849

Axiom
annotated source: prepupal stage P1
annotated property: hasExactSynonym
annotated target: white puparium stage
database_cross_reference: FlyBase:FBrf0036849

Axiom
annotated source: prepupal stage P1
annotated property: hasNarrowSynonym
annotated target: pupal stage P0
database_cross_reference: FlyBase:FBrf0036849

Axiom
annotated source: prepupal stage P1
annotated property: hasNarrowSynonym
annotated target: white prepupa
database_cross_reference: FlyBase:FBrf0036849

prepupal stage P2
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: prepupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P1
definition: Male gonads become less distinct. Oral armature stops moving permanently. Dorsal medial abdominal contractions stop. Gas bubble becomes visible within abdomen. Duration at 25 degrees C: approximately 100 minutes. (120.3-122 hours after egg laying; 0.3-2 hours after puparium formation).
has exact synonym: brown puparium stage
has exact synonym: pupal stage P2
has OBO namespace: FlyBase_development_CV
id: FBdv:00005344
comment: Temporal ordering number - 520.

Axiom
annotated source: prepupal stage P2
annotated property: definition
annotated target: Male gonads become less distinct. Oral armature stops moving permanently. Dorsal medial abdominal contractions stop. Gas bubble becomes visible within abdomen. Duration at 25 degrees C: approximately 100 minutes. (120.3-122 hours after egg laying; 0.3-2 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: prepupal stage P2
annotated property: hasExactSynonym
annotated target: brown puparium stage
database_cross_reference: FlyBase:FBrf0036849

prepupal stage P3
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: prepupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P2
definition: Ridge of the operculum becomes distinct. Puparium begins to separate from underlying epidermis. Becomes positively buoyant. Duration at 25 degrees C: approximately 4 hours, 45 minutes. (122-126.75 hours after egg laying; 2-6.75 hours after puparium formation).
has exact synonym: bubble prepupa stage
has exact synonym: pupal stage P3
has OBO namespace: FlyBase_development_CV
id: FBdv:00005345
comment: Temporal ordering number - 530.

Axiom
annotated source: prepupal stage P3
annotated property: definition
annotated target: Ridge of the operculum becomes distinct. Puparium begins to separate from underlying epidermis. Becomes positively buoyant. Duration at 25 degrees C: approximately 4 hours, 45 minutes. (122-126.75 hours after egg laying; 2-6.75 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: prepupal stage P3
annotated property: hasExactSynonym
annotated target: bubble prepupa stage
database_cross_reference: FlyBase:FBrf0036849

prepupal stage P4
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: prepupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P3
definition: Prepupal stage P4 begins as the lateral trunk trachea become obscured and ends when the imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 5 hours, 30 minutes. (126.75-132.2 hours after egg laying; 6.75-12.2 hours after puparium formation).
has exact synonym: cryptocephalic pupa
has exact synonym: pupal stage P4
has OBO namespace: FlyBase_development_CV
id: FBdv:00005346
comment: Temporal ordering number - 540.

Axiom
annotated source: prepupal stage P4
annotated property: definition
annotated target: Prepupal stage P4 begins as the lateral trunk trachea become obscured and ends when the imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 5 hours, 30 minutes. (126.75-132.2 hours after egg laying; 6.75-12.2 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: prepupal stage P4
annotated property: hasExactSynonym
annotated target: cryptocephalic pupa
database_cross_reference: FlyBase:FBrf0036849

prepupal stage P4(i)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: prepupal stage P4
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P3
definition: Lateral trunk tracheae become obscured. Dorsal medial abdominal contractions occur. Everted leg and wing discs become visible. Bubble appears in posterior of puparium, displacing the pupa anteriorly; abdominal bubble disappears. Duration at 25 degrees C: approximately 5 hours, 15 minutes. (126.75-132 hours after egg laying; 6.75-12 hours after puparium formation).
has exact synonym: buoyant stage
has exact synonym: pupal stage P4(i)
has OBO namespace: FlyBase_development_CV
id: FBdv:00005347
comment: Temporal ordering number - 550.

Axiom
annotated source: prepupal stage P4(i)
annotated property: definition
annotated target: Lateral trunk tracheae become obscured. Dorsal medial abdominal contractions occur. Everted leg and wing discs become visible. Bubble appears in posterior of puparium, displacing the pupa anteriorly; abdominal bubble disappears. Duration at 25 degrees C: approximately 5 hours, 15 minutes. (126.75-132 hours after egg laying; 6.75-12 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: prepupal stage P4(i)
annotated property: hasExactSynonym
annotated target: buoyant stage
database_cross_reference: FlyBase:FBrf0036849

prepupal stage P4(ii)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: prepupal stage P4
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P4(i)
definition: Bubble is displaced to anterior end of the puparium, and pupa withdraws to the posterior end. Imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 12 minutes. (132-132.2 hours after egg laying; 12-12.2 hours after puparium formation).
has exact synonym: moving bubble stage
has exact synonym: pupal stage P4(ii)
has OBO namespace: FlyBase_development_CV
id: FBdv:00005348
comment: Temporal ordering number - 560.

Axiom
annotated source: prepupal stage P4(ii)
annotated property: definition
annotated target: Bubble is displaced to anterior end of the puparium, and pupa withdraws to the posterior end. Imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 12 minutes. (132-132.2 hours after egg laying; 12-12.2 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: prepupal stage P4(ii)
annotated property: hasExactSynonym
annotated target: moving bubble stage
database_cross_reference: FlyBase:FBrf0036849

pupal stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: substage of
  some values from: P-stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage
subclass of: Restriction
  on property: immediately precedes
  some values from: pharate adult stage
definition: The pupal stage starts once larval/pupal apolysis is complete as indicated by the expulsion of the larval armature. Early in this stage, the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. Duration at 25 degrees C: approximately 32 hours. (132.2-164.3 hours after egg laying; 12.2-44.3 hours after puparium formation).
has exact synonym: phanerocephalic pupa
has OBO namespace: FlyBase_development_CV
id: FBdv:00005349
comment: Temporal ordering number - 570. DISAMBIGUATION: In Drosophila lab vernacular, the term 'pupal stage' is often used to refer to the entire period from formation of the puparium to eclosion. However, this does not correspond to the standard usage of 'pupal stage' for Cyclorrhaphous flies (for discussion see: FBrf0087128). Briefly: formation of the puparium (hardening of the larval cuticle) marks the beginning of the pre-pupal stage. The pupal stage begins following pupal/larval apolysis - detachment of the larval epidermis from the puparium. In Drosophila, the outward sign of the completion of apolysis is the eversion of the head and expulsion of the larval mouthparts (FBrf0036849). We use P-stage to refer to the stage from pupariation to eclosion, and restrict pupal stage to its standard usage.

Axiom
annotated source: pupal stage
annotated property: definition
annotated target: The pupal stage starts once larval/pupal apolysis is complete as indicated by the expulsion of the larval armature. Early in this stage, the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. Duration at 25 degrees C: approximately 32 hours. (132.2-164.3 hours after egg laying; 12.2-44.3 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pupal stage
annotated property: hasExactSynonym
annotated target: phanerocephalic pupa
database_cross_reference: FlyBase:FBrf0036849

pupal stage P5
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P4
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P4(ii)
definition: Pupal stage P5 starts when the legs and wings reach full extension along the abdomen and ends as the Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 6 hours, 30 minutes. (132.2-138.7 hours after egg laying; 12.2-18.7 hours after puparium formation).
has OBO namespace: FlyBase_development_CV
id: FBdv:00005350
comment: Temporal ordering number - 580.

Axiom
annotated source: pupal stage P5
annotated property: definition
annotated target: Pupal stage P5 starts when the legs and wings reach full extension along the abdomen and ends as the Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 6 hours, 30 minutes. (132.2-138.7 hours after egg laying; 12.2-18.7 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

pupal stage P5(i)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pupal stage P5
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P4
subclass of: Restriction
  on property: immediately preceded by
  some values from: prepupal stage P4(ii)
definition: Legs and wings reach full extension along abdomen. Enlarged initial segments of anterior pair Malpighian tubules move from thorax into abdomen. Translucent patch that lacks adhering fat body cells becomes discernible in the middle of the eye region. Pair of white Malpighian tubules becomes visible dorsally in the abdomen. Duration at 25 degrees C: approximately 66 minutes. (132.2-133.3 hours after egg laying; 12.2-13.3 hours after puparium formation).
has exact synonym: Malpighian tubules migrating
has OBO namespace: FlyBase_development_CV
id: FBdv:00005351
comment: Temporal ordering number - 590.

Axiom
annotated source: pupal stage P5(i)
annotated property: definition
annotated target: Legs and wings reach full extension along abdomen. Enlarged initial segments of anterior pair Malpighian tubules move from thorax into abdomen. Translucent patch that lacks adhering fat body cells becomes discernible in the middle of the eye region. Pair of white Malpighian tubules becomes visible dorsally in the abdomen. Duration at 25 degrees C: approximately 66 minutes. (132.2-133.3 hours after egg laying; 12.2-13.3 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pupal stage P5(i)
annotated property: hasExactSynonym
annotated target: Malpighian tubules migrating
database_cross_reference: FlyBase:FBrf0036849

pupal stage P5(ii)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pupal stage P5
subclass of: Restriction
  on property: immediately preceded by
  some values from: pupal stage P5(i)
definition: Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 5 hours, 25 minutes. (133.3-138.7 hours after egg laying; 13.3-18.7 hours after puparium formation).
has exact synonym: white Malpighian tubules stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005352
comment: Temporal ordering number - 600.

Axiom
annotated source: pupal stage P5(ii)
annotated property: definition
annotated target: Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 5 hours, 25 minutes. (133.3-138.7 hours after egg laying; 13.3-18.7 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pupal stage P5(ii)
annotated property: hasExactSynonym
annotated target: white Malpighian tubules stage
database_cross_reference: FlyBase:FBrf0036849

pupal stage P6
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pupal stage P5
subclass of: Restriction
  on property: immediately preceded by
  some values from: pupal stage P5(ii)
definition: Dark green 'yellow body' appears between the anterior ends of the two Malpighian tubule segments, mid-dorsally at the anterior of the abdomen. Duration at 25 degrees C: approximately 13 hours, 45 minutes. (138.7-152.4 hours after egg laying; 18.7-32.4 hours after puparium formation).
has exact synonym: green Malpighian tubules stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005353
comment: Temporal ordering number - 610.

Axiom
annotated source: pupal stage P6
annotated property: definition
annotated target: Dark green 'yellow body' appears between the anterior ends of the two Malpighian tubule segments, mid-dorsally at the anterior of the abdomen. Duration at 25 degrees C: approximately 13 hours, 45 minutes. (138.7-152.4 hours after egg laying; 18.7-32.4 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pupal stage P6
annotated property: hasExactSynonym
annotated target: green Malpighian tubules stage
database_cross_reference: FlyBase:FBrf0036849

pupal stage P7
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pupal stage P6
definition: The 'yellow body' moves back between the Malpighian tubules. The transparent pupal cuticle separates from the underlying epidermis. Eye cup becomes yellow at its perimeter. Duration at 25 degrees C: approximately 12 hours. (152.4-164.3 hours after egg laying; 32.4-44.3 hours after puparium formation).
has exact synonym: yellow body stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005354
comment: Temporal ordering number - 620.

Axiom
annotated source: pupal stage P7
annotated property: definition
annotated target: The 'yellow body' moves back between the Malpighian tubules. The transparent pupal cuticle separates from the underlying epidermis. Eye cup becomes yellow at its perimeter. Duration at 25 degrees C: approximately 12 hours. (152.4-164.3 hours after egg laying; 32.4-44.3 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pupal stage P7
annotated property: hasExactSynonym
annotated target: yellow body stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P8
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pupal stage P7
definition: Pale yellow pigmentation spreads inwards across the eye. Eye color becomes bright yellow, then changes to amber. Duration at 25 degrees C: approximately 12 hours 20 minutes. (164.3-176.6 hours after egg laying; 44.3-56.6 hours after puparium formation).
has exact synonym: pupal stage P8
has exact synonym: yellow-eyed stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005355
comment: Temporal ordering number - 630.

Axiom
annotated source: pharate adult stage P8
annotated property: definition
annotated target: Pale yellow pigmentation spreads inwards across the eye. Eye color becomes bright yellow, then changes to amber. Duration at 25 degrees C: approximately 12 hours 20 minutes. (164.3-176.6 hours after egg laying; 44.3-56.6 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P8
annotated property: hasExactSynonym
annotated target: yellow-eyed stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P9
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P8
definition: Eye color darkens to deep amber, then becomes pale pink. Duration at 25 degrees C: approximately 18 hours. (176.6-194.5 hours after egg laying; 56.6-74.5 hours after puparium formation).
has exact synonym: amber-eyed stage
has exact synonym: pupal stage P9
has OBO namespace: FlyBase_development_CV
id: FBdv:00005356
comment: Temporal ordering number - 640.

Axiom
annotated source: pharate adult stage P9
annotated property: definition
annotated target: Eye color darkens to deep amber, then becomes pale pink. Duration at 25 degrees C: approximately 18 hours. (176.6-194.5 hours after egg laying; 56.6-74.5 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P9
annotated property: hasExactSynonym
annotated target: amber-eyed stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P10
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P9
definition: Eyes become bright red. Orbital and ocellar bristles and vibrissae darken. Duration at 25 degrees C: approximately 6 minutes. (194.5-194.6 hours after egg laying; 74.5-74.6 hours after puparium formation).
has exact synonym: pupal stage P10
has exact synonym: red-eye bald stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005357
comment: Temporal ordering number - 650.

Axiom
annotated source: pharate adult stage P10
annotated property: definition
annotated target: Eyes become bright red. Orbital and ocellar bristles and vibrissae darken. Duration at 25 degrees C: approximately 6 minutes. (194.5-194.6 hours after egg laying; 74.5-74.6 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P10
annotated property: hasExactSynonym
annotated target: red-eye bald stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P11
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P10
definition: Thoracic bristles become visible, and the tips of the wings turn grey. Duration at 25 degrees C: approximately 2 hours. (194.6-196.6 hours after egg laying; 74.6-76.6 hours after puparium formation).
has exact synonym: pupal stage P11
has OBO namespace: FlyBase_development_CV
id: FBdv:00005358
comment: Temporal ordering number - 660.

Axiom
annotated source: pharate adult stage P11
annotated property: definition
annotated target: Thoracic bristles become visible, and the tips of the wings turn grey. Duration at 25 degrees C: approximately 2 hours. (194.6-196.6 hours after egg laying; 74.6-76.6 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

pharate adult stage P11(i)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage P11
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P10
definition: Dorsal thoracic microchaetes and macrochaetes become visible. Duration at 25 degrees C: approximately 80 minutes (194.6-195.5 hours after egg laying; 74.6-75.9 hours after puparium formation).
has exact synonym: head bristles stage
has exact synonym: pupal stage P11(i)
has OBO namespace: FlyBase_development_CV
id: FBdv:00005359
comment: Temporal ordering number - 670.

Axiom
annotated source: pharate adult stage P11(i)
annotated property: definition
annotated target: Dorsal thoracic microchaetes and macrochaetes become visible. Duration at 25 degrees C: approximately 80 minutes (194.6-195.5 hours after egg laying; 74.6-75.9 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P11(i)
annotated property: hasExactSynonym
annotated target: head bristles stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P11(ii)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage P11
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P11(i)
definition: Tips of folded wings become grey. Duration at 25 degrees C: approximately 45 minutes (195.5-196.6 hours after egg laying; 75.9-76.6 hours after puparium formation).
has exact synonym: pupal stage P11(ii)
has exact synonym: thoracic bristles stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005360
comment: Temporal ordering number - 680.

Axiom
annotated source: pharate adult stage P11(ii)
annotated property: definition
annotated target: Tips of folded wings become grey. Duration at 25 degrees C: approximately 45 minutes (195.5-196.6 hours after egg laying; 75.9-76.6 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P11(ii)
annotated property: hasExactSynonym
annotated target: thoracic bristles stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P12
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P11
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P11(ii)
definition: Pharate adult stage P12 begins as the abdominal tergite bristles become visible, and ends as the wings darken to black. Duration at 25 degrees C: approximately 2 hours. (196.6-198.6 hours after egg laying; 76.6-78.6 hours after puparium formation).
has exact synonym: pupal stage P12
has OBO namespace: FlyBase_development_CV
id: FBdv:00005361
comment: Temporal ordering number - 690.

Axiom
annotated source: pharate adult stage P12
annotated property: definition
annotated target: Pharate adult stage P12 begins as the abdominal tergite bristles become visible, and ends as the wings darken to black. Duration at 25 degrees C: approximately 2 hours. (196.6-198.6 hours after egg laying; 76.6-78.6 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

pharate adult stage P12(i)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage P12
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P11
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P11(ii)
definition: Bristles of the abdominal tergites become visible, and the wings become grey. Duration at 25 degrees C: approximately 55 minutes. (196.6-197.5 hours after egg laying; 76.6-77.5 hours after puparium formation).
has exact synonym: pupal stage P12(i)
has exact synonym: wing tips grey stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005362
comment: Temporal ordering number - 700.

Axiom
annotated source: pharate adult stage P12(i)
annotated property: definition
annotated target: Bristles of the abdominal tergites become visible, and the wings become grey. Duration at 25 degrees C: approximately 55 minutes. (196.6-197.5 hours after egg laying; 76.6-77.5 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P12(i)
annotated property: hasExactSynonym
annotated target: wing tips grey stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P12(ii)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage P12
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P12(i)
definition: Sex combs darken in males. Wings darken to black. Duration at 25 degrees C: approximately 65 minutes. (197.5-198.6 hours after egg laying; 77.5-78.6 hours after puparium formation).
has exact synonym: pupal stage P12(ii)
has exact synonym: wings grey stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005363
comment: Temporal ordering number - 710.

Axiom
annotated source: pharate adult stage P12(ii)
annotated property: definition
annotated target: Sex combs darken in males. Wings darken to black. Duration at 25 degrees C: approximately 65 minutes. (197.5-198.6 hours after egg laying; 77.5-78.6 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P12(ii)
annotated property: hasExactSynonym
annotated target: wings grey stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P13
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P12
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P12(ii)
definition: Tarsal bristles darken and claws become black. Duration at 25 degrees C: approximately 3 hours, 20 minutes. (198.6-201.9 hours after egg laying; 78.6-81.9 hours after puparium formation).
has exact synonym: pupal stage P13
has exact synonym: wings black stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00005364
comment: Temporal ordering number - 720.

Axiom
annotated source: pharate adult stage P13
annotated property: definition
annotated target: Tarsal bristles darken and claws become black. Duration at 25 degrees C: approximately 3 hours, 20 minutes. (198.6-201.9 hours after egg laying; 78.6-81.9 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P13
annotated property: hasExactSynonym
annotated target: wings black stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P14
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P13
definition: The meconium appears dorsally at the posterior tip of the abdomen. Duration at 25 degrees C: approximately 9 hours, 30 minutes (201.9-211.5 hours after egg laying; 81.9-91.5 hours after puparium formation).
has exact synonym: mature bristles stage
has exact synonym: pupal stage P14
has OBO namespace: FlyBase_development_CV
id: FBdv:00005365
comment: Temporal ordering number - 730.

Axiom
annotated source: pharate adult stage P14
annotated property: definition
annotated target: The meconium appears dorsally at the posterior tip of the abdomen. Duration at 25 degrees C: approximately 9 hours, 30 minutes (201.9-211.5 hours after egg laying; 81.9-91.5 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P14
annotated property: hasExactSynonym
annotated target: mature bristles stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P15
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P14
definition: Pharate adult stage P15 begins with the tanning of the tergites and ends with eclosion. Duration at 25 degrees C: approximately 8 hours, 30 minutes. (211.5-220 hours after egg laying; 91.5-100 hours after puparium formation).
has exact synonym: pupal stage P15
has OBO namespace: FlyBase_development_CV
id: FBdv:00005366
comment: Temporal ordering number - 740.

Axiom
annotated source: pharate adult stage P15
annotated property: definition
annotated target: Pharate adult stage P15 begins with the tanning of the tergites and ends with eclosion. Duration at 25 degrees C: approximately 8 hours, 30 minutes. (211.5-220 hours after egg laying; 91.5-100 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

pharate adult stage P15(i)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage P15
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P14
definition: Tanning of the tergites obscures the Malpighian tubules and the 'yellow body'. Legs begin to twitch; fly is able to walk if puparium is removed prematurely. Ptilinum expands by hydrostatic pressure, opening the operculum. Duration at 25 degrees C: approximately 8 hours, 6 minutes. (211.5-219.6 hours after egg laying; 91.5-99.6 hours after puparium formation).
has exact synonym: meconium stage
has exact synonym: pupal stage P15(i)
has OBO namespace: FlyBase_development_CV
id: FBdv:00005367
comment: Temporal ordering number - 750.

Axiom
annotated source: pharate adult stage P15(i)
annotated property: definition
annotated target: Tanning of the tergites obscures the Malpighian tubules and the 'yellow body'. Legs begin to twitch; fly is able to walk if puparium is removed prematurely. Ptilinum expands by hydrostatic pressure, opening the operculum. Duration at 25 degrees C: approximately 8 hours, 6 minutes. (211.5-219.6 hours after egg laying; 91.5-99.6 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P15(i)
annotated property: hasExactSynonym
annotated target: meconium stage
database_cross_reference: FlyBase:FBrf0036849

pharate adult stage P15(ii)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: pharate adult stage P15
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P15(i)
definition: Stage which starts when the operculum opens and ends when eclosion is completed. Duration at 25 degrees C: approximately 24 minutes. (219.6-220 hours after egg laying; 99.6-100 hours after puparium formation).
has exact synonym: eclosion stage
has exact synonym: pupal stage P15(ii)
has OBO namespace: FlyBase_development_CV
id: FBdv:00005368
comment: Temporal ordering number - 760.

Axiom
annotated source: pharate adult stage P15(ii)
annotated property: definition
annotated target: Stage which starts when the operculum opens and ends when eclosion is completed. Duration at 25 degrees C: approximately 24 minutes. (219.6-220 hours after egg laying; 99.6-100 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355

Axiom
annotated source: pharate adult stage P15(ii)
annotated property: hasExactSynonym
annotated target: eclosion stage
database_cross_reference: FlyBase:FBrf0036849

adult stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P15
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P15(ii)
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: P-stage
definition: The stage of the Drosophila life-cycle from eclosion to death.
has OBO namespace: FlyBase_development_CV
id: FBdv:00005369
comment: Temporal ordering number - 770.

Axiom
annotated source: adult stage
annotated property: definition
annotated target: The stage of the Drosophila life-cycle from eclosion to death.
database_cross_reference: FBC:DOS

adult stage A1
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: immature adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P15(ii)
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: P-stage
subclass of: Restriction
  on property: immediately precedes
  some values from: adult stage A2
definition: Newly eclosed adult stage. Animal free of pupal case. Runs rapidly to find site for wing expansion. Wings are folded back and black against a very pale abdomen.
has alternative id: FBdv:00005373
has OBO namespace: FlyBase_development_CV
has related synonym: adult stage I
id: FBdv:00005370
comment: Temporal ordering number - 785. The time at which eclosed flies settle down for wing expansion can vary greatly. If they fail to find a suitable site then expansion can be delayed by several hours.

Axiom
annotated source: adult stage A1
annotated property: definition
annotated target: Newly eclosed adult stage. Animal free of pupal case. Runs rapidly to find site for wing expansion. Wings are folded back and black against a very pale abdomen.
database_cross_reference: FlyBase:FBrf0049147

adult stage A2
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: immature adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: adult stage A1
subclass of: Restriction
  on property: immediately precedes
  some values from: adult stage A3
definition: Stage, shortly after eclosion, during which the wings expand. During wing expansion, the abdomen pulsates and the hind legs stroke the wings vigorously for several minutes at a time. The stage ends when the wings are folded down over the abdomen, which has become broader and shorter, and the wing cuticle has lost its folds. The stage lasts around 15 minutes at 25'C.
has alternative id: FBdv:00005374
has OBO namespace: FlyBase_development_CV
has related synonym: adult stage II
id: FBdv:00005371
comment: Temporal ordering number - 790.

Axiom
annotated source: adult stage A2
annotated property: definition
annotated target: Stage, shortly after eclosion, during which the wings expand. During wing expansion, the abdomen pulsates and the hind legs stroke the wings vigorously for several minutes at a time. The stage ends when the wings are folded down over the abdomen, which has become broader and shorter, and the wing cuticle has lost its folds. The stage lasts around 15 minutes at 25'C.
database_cross_reference: FlyBase:FBrf0049147

pharate adult stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: substage of
  some values from: P-stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pupal stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pupal stage P7
subclass of: Restriction
  on property: immediately precedes
  some values from: adult stage
subclass of: Restriction
  on property: immediately precedes
  some values from: adult stage A1
subclass of: Restriction
  on property: immediately precedes
  some values from: immature adult stage
definition: The developing adult after pupal-adult apolysis, i.e.- from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion. Duration at 25 degrees C: approximately 55.7 hours (164.3-220 hours after egg laying; 44.3-100 hours after puparium formation).
has OBO namespace: FlyBase_development_CV
id: FBdv:00006011
comment: Temporal ordering number - 625.

Axiom
annotated source: pharate adult stage
annotated property: definition
annotated target: The developing adult after pupal-adult apolysis, i.e.- from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion. Duration at 25 degrees C: approximately 55.7 hours (164.3-220 hours after egg laying; 44.3-100 hours after puparium formation).
database_cross_reference: FlyBase:FBrf0036849
database_cross_reference: FlyBase:FBrf0048355
database_cross_reference: FlyBase:FBrf0049147

adult stage A3
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: immature adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: adult stage A2
subclass of: Restriction
  on property: immediately precedes
  some values from: mature adult stage
definition: Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C.
has alternative id: FBdv:00005375
has OBO namespace: FlyBase_development_CV
has related synonym: adult stage III
id: FBdv:00006012
comment: Temporal ordering number - 800.

Axiom
annotated source: adult stage A3
annotated property: definition
annotated target: Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C.
database_cross_reference: FlyBase:FBrf0049147

P-stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar larval stage L2
subclass of: Restriction
  on property: immediately preceded by
  some values from: late third instar larval stage
subclass of: Restriction
  on property: immediately precedes
  some values from: adult stage
subclass of: Restriction
  on property: immediately precedes
  some values from: adult stage A1
subclass of: Restriction
  on property: immediately precedes
  some values from: immature adult stage
definition: The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2008-06-05T04:51:40Z
has broad synonym: metamorphosis
has OBO namespace: FlyBase_development_CV
has related synonym: pupal stage
id: FBdv:00007001
comment: Temporal ordering number - 490. DISAMBIGUATION: In Drosophila lab vernacular, the term 'pupal stage' is often used to refer to the entire period from formation of the puparium to eclosion. However, this does not correspond to the standard usage of 'pupal stage' for cyclorrhaphous flies (for discussion see: FBrf0087128). Briefly: formation of the puparium (hardening of the larval cuticle) marks the beginning of the pre-pupal stage. The pupal stage begins following pupal/larval apolysis - detachment of the larval epidermis from the puparium. In Drosophila, the outward sign of the completion of apolysis is the eversion of the head an expulsion of the larval mouthparts (FBrf0036849). We use P-stage to refer to the stage from pupariation to eclosion, and restrict pupal stage to its standard usage.

Axiom
annotated source: P-stage
annotated property: definition
annotated target: The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion.
database_cross_reference: FBC:DOS

third instar larval stage L1
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: late third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: wandering third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar - cleared gut stage
definition: Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage.
has OBO namespace: FlyBase_development_CV
id: FBdv:00007004
comment: Temporal ordering number - 470.

Axiom
annotated source: third instar larval stage L1
annotated property: definition
annotated target: Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage.
database_cross_reference: FlyBase:FBrf0036849

third instar larval stage L2
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: late third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar larval stage L1
definition: The anterior spiracles are fully everted, with 7-9 finger-like projections. The body shortens, withdrawing three apparent abdominal segments and the larva sticks to its substrate.
has exact synonym: spiracles everted larva
has OBO namespace: FlyBase_development_CV
has related synonym: white prepupa
id: FBdv:00007005
comment: Temporal ordering number - 480.

Axiom
annotated source: third instar larval stage L2
annotated property: definition
annotated target: The anterior spiracles are fully everted, with 7-9 finger-like projections. The body shortens, withdrawing three apparent abdominal segments and the larva sticks to its substrate.
database_cross_reference: FlyBase:FBrf0036849

Axiom
annotated source: third instar larval stage L2
annotated property: hasExactSynonym
annotated target: spiracles everted larva
database_cross_reference: FlyBase:FBrf0036849

Axiom
annotated source: third instar larval stage L2
annotated property: hasRelatedSynonym
annotated target: white prepupa
database_cross_reference: FlyBase:FBrf0036849

late third instar larval stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: early third instar larval stage
definition: Third instar larva from the beginning of wandering to the beginning of puparium formation.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2008-12-11T01:19:53Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007007
comment: Temporal ordering number - 450.

Axiom
annotated source: late third instar larval stage
annotated property: definition
annotated target: Third instar larva from the beginning of wandering to the beginning of puparium formation.
database_cross_reference: FBC:DOS

developmental process
type: Class
subclass of: biological process
definition: A biological process whose specific outcome is the progression of an integrated living unit (an anatomical structure or an entire organism) over time from an initial condition to a later condition.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2009-10-01T05:56:42Z
database_cross_reference: GO:0032502
has OBO namespace: FlyBase_development_CV
id: FBdv:00007009

Axiom
annotated source: developmental process
annotated property: definition
annotated target: A biological process whose specific outcome is the progression of an integrated living unit (an anatomical structure or an entire organism) over time from an initial condition to a later condition.
database_cross_reference: GO:0032502

embryonic cycle
type: Class
subclass of: biological process
subclass of: GO_0045448
definition: A cycle of nuclear division during the embryogenesis of Drosophila melanogaster. The first 13 cycles are synchronous throughout the embryo and occur their timing relative to other developmental processes is invariant. Later nuclear division cycles are asynchronous across the embryo although may be more locally synchronized.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2009-10-01T05:57:41Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007011

Axiom
annotated source: embryonic cycle
annotated property: definition
annotated target: A cycle of nuclear division during the embryogenesis of Drosophila melanogaster. The first 13 cycles are synchronous throughout the embryo and occur their timing relative to other developmental processes is invariant. Later nuclear division cycles are asynchronous across the embryo although may be more locally synchronized.
database_cross_reference: FlyBase:FBrf0049535
database_cross_reference: FlyBase:FBrf0089570

life stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: Drosophila life
definition: A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2009-10-01T05:59:22Z
has exact synonym: life cycle stage
has OBO namespace: FlyBase_development_CV
id: FBdv:00007012

Axiom
annotated source: life stage
annotated property: definition
annotated target: A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion.
database_cross_reference: FBC:DOS

age
type: Class
subclass of: BFO_0000003
definition: Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2010-09-29T12:25:36Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007013

Axiom
annotated source: age
annotated property: definition
annotated target: Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion.
database_cross_reference: FBC:DOS

adult age in days
type: Class
subclass of: age
definition: Temporal subdivision of adulthood in days post-eclosion.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2010-09-29T12:28:05Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007014

Axiom
annotated source: adult age in days
annotated property: definition
annotated target: Temporal subdivision of adulthood in days post-eclosion.
database_cross_reference: FBC:DOS

embryonic stage 17(i)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 17
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 16
definition: The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying).
contributor: http://orcid.org/0000-0002-7073-9172
date: 2011-04-26T11:57:15Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007015
comment: Temporal ordering number - 391. Should not be used to stage embryos whose development is at temperatures other than 25'C.

Axiom
annotated source: embryonic stage 17(i)
annotated property: definition
annotated target: The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying).
database_cross_reference: FBC:DOS

embryonic stage 17(ii)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 17
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 17(i)
definition: Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying).
contributor: http://orcid.org/0000-0002-7073-9172
date: 2011-04-26T12:00:15Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007016
comment: Temporal ordering number - 392. Should not be used to stage embryos whose development is at temperatures other than 25'C.

Axiom
annotated source: embryonic stage 17(ii)
annotated property: definition
annotated target: Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying).
database_cross_reference: FBC:DOS

embryonic stage 17(iii)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 17
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 17(ii)
definition: Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying).
contributor: http://orcid.org/0000-0002-7073-9172
date: 2011-04-26T12:01:18Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007017
comment: Temporal ordering number - 393. Should not be used to stage embryos whose development is at temperatures other than 25'C.

Axiom
annotated source: embryonic stage 17(iii)
annotated property: definition
annotated target: Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying).
database_cross_reference: FBC:DOS

embryonic stage 17(iv)
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: embryonic stage 17
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 17(iii)
definition: Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying).
contributor: http://orcid.org/0000-0002-7073-9172
date: 2011-04-26T12:03:14Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007018
comment: Temporal ordering number - 394. Should not be used to stage embryos whose development is at temperatures other than 25'C.

Axiom
annotated source: embryonic stage 17(iv)
annotated property: definition
annotated target: Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying).
database_cross_reference: FBC:DOS

third instar - uncleared gut stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: wandering third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: early third instar larval stage
definition: The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut.
has OBO namespace: FlyBase_development_CV
id: FBdv:00007019
comment: Temporal ordering number - 462. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with the same color guts (dark blue) as feeding larvae (Andres and Thummel, 1994). Larvae at this stage are in chromosomal puff stage 1 (Andres and Thummel, 1994).

Axiom
annotated source: third instar - uncleared gut stage
annotated property: definition
annotated target: The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut.
database_cross_reference: FlyBase:FBrf0076598

third instar - partially cleared gut stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: wandering third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar - uncleared gut stage
definition: The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents.
has OBO namespace: FlyBase_development_CV
id: FBdv:00007020
comment: Temporal ordering number - 465. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with lighter colored guts (light blue) than feeding larvae (Andres and Thummel, 1994). Larvae at this stage are mainly in chromosomal puff stages 2-7 (Andres and Thummel, 1994).

Axiom
annotated source: third instar - partially cleared gut stage
annotated property: definition
annotated target: The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents.
database_cross_reference: FlyBase:FBrf0076598

third instar - cleared gut stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: wandering third instar larval stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: third instar - partially cleared gut stage
definition: The substage of the wandering third instar larval stage when the larva has cleared its gut contents.
has OBO namespace: FlyBase_development_CV
id: FBdv:00007021
comment: Temporal ordering number - 467. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with guts lacking any blue stain (Andres and Thummel, 1994). Larvae at this stage are mainly in chromosomal puff stages 7-9 and pupate within 1-6 hours (Andres and Thummel, 1994.

Axiom
annotated source: third instar - cleared gut stage
annotated property: definition
annotated target: The substage of the wandering third instar larval stage when the larva has cleared its gut contents.
database_cross_reference: FlyBase:FBrf0076598

biological process
type: Class
subclass of: BFO_0000003
definition: The execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module.
database_cross_reference: GO:0008150
has OBO namespace: FlyBase_development_CV
id: FBdv:00007024

Axiom
annotated source: biological process
annotated property: definition
annotated target: The execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module.
database_cross_reference: GO:0008150

immature adult stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: substage of
  some values from: day 0 of adulthood
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: P-stage
subclass of: Restriction
  on property: immediately precedes
  some values from: mature adult stage
definition: The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3).
contributor: http://orcid.org/0000-0002-7073-9172
date: 2013-01-08T20:06:59Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007025
comment: Temporal ordering number - 782.

Axiom
annotated source: immature adult stage
annotated property: definition
annotated target: The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3).
database_cross_reference: FBC:DOS

mature adult stage
type: Class
subclass of: life stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: adult stage A3
subclass of: Restriction
  on property: immediately preceded by
  some values from: immature adult stage
definition: Life stage from the end of adult stage A3, when tanning is complete, to death.
contributor: http://orcid.org/0000-0002-7073-9172
date: 2013-01-10T13:03:54Z
has OBO namespace: FlyBase_development_CV
id: FBdv:00007026

Axiom
annotated source: mature adult stage
annotated property: definition
annotated target: Life stage from the end of adult stage A3, when tanning is complete, to death.
database_cross_reference: FBC:DOS

day 0 of adulthood
type: Class
subclass of: adult age in days
subclass of: Restriction
  on property: substage of
  some values from: adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P15
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage P15(ii)
subclass of: Restriction
  on property: immediately preceded by
  some values from: pharate adult stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: P-stage
definition: The day of eclosion.
has OBO namespace: FlyBase_development_CV
id: FBdv:00007075
comment: Temporal ordering number - 780.

Axiom
annotated source: day 0 of adulthood
annotated property: definition
annotated target: The day of eclosion.
database_cross_reference: FBC:DOS

early extended germ band stage
type: Class
subclass of: developmental stage
subclass of: Restriction
  on property: substage of
  some values from: extended germ band stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: gastrula stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: embryonic stage 8
definition: A collective term for stages 9 and 10.
has OBO namespace: FlyBase_development_CV
id: FBdv:00014201
comment: Temporal ordering number - 270.

Axiom
annotated source: early extended germ band stage
annotated property: definition
annotated target: A collective term for stages 9 and 10.
database_cross_reference: FBC:DOS

Drosophila melanogaster
type: Class
subclass of: invertebrate
IAO_0000111: Drosophila melanogaster
IAO_0000118: Sophophora melanogaster
IAO_0000118: fruit fly
IAO_0000412: ncbitaxon.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: IAO_0000104
subclass of: BFO_0000015
IAO_0000111: planned process
IAO_0000112: Injecting mice with a vaccine in order to test its efficacy
IAO_0000114: IAO_0000122
definition: A process that realizes a plan which is the concretization of a plan specification.
IAO_0000116: '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.)
IAO_0000116: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
IAO_0000117: Bjoern Peters
IAO_0000119: branch derived
IAO_0000232: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
IAO_0000232: 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)

specimen role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
IAO_0000111: specimen role
IAO_0000112: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
IAO_0000114: IAO_0000122
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
IAO_0000116: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
IAO_0000116: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
IAO_0000116: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
IAO_0000116: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI
IAO_0000233: https://github.com/obi-ontology/obi/issues/1013

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: BFO_0000040
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
IAO_0000111: specimen collection process
IAO_0000112: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
IAO_0000114: IAO_0000122
definition: A planned process with the objective of collecting a specimen.
IAO_0000116: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
IAO_0000116: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
IAO_0000116: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
IAO_0000116: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
IAO_0000117: Bjoern Peters
IAO_0000118: specimen collection
IAO_0000232: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
IAO_0000232: 6/9/09: used at workshop

specimen collection objective
type: Class
subclass of: IAO_0000005
IAO_0000111: specimen collection objective
IAO_0000112: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
IAO_0000114: IAO_0000122
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

collection of specimens
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: has member
    all values from: specimen
subclass of: BFO_0000040
IAO_0000111: collection of specimens
IAO_0000112: Blood cells collected from multiple donors over the course of a study.
IAO_0000114: IAO_0000125
definition: A material entity that has two or more specimens as its parts.
IAO_0000116: Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: OBIB, OBI

specimen
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: BFO_0000040
IAO_0000111: specimen
IAO_0000112: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
IAO_0000114: IAO_0000122
definition: A material entity that has the specimen role.
IAO_0000116: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000119: GROUP: OBI Biomaterial Branch
IAO_0000233: https://github.com/obi-ontology/obi/issues/1013

anatomical entity
type: Class
definition: 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.
IAO_0000412: uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1515976
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FBbt:10000000
database_cross_reference: FBbt_root:00000000
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
has OBO namespace: uberon
id: UBERON:0001062
in subset: upper level

eukaryote
type: Class
subclass of: cellular organisms
definition: This includes fungi, vertebrates and invertebrates. Eukaryotic cells have a well-defined nucleus and membrane enveloped organelles namely, mitochondria, endoplasmic reticulum, golgi apparatus, and lysosomes.

invertebrate
type: Class
subclass of: metazoa
definition: These animals lack a vertebral column and many of which are used as model organisms in HTS screening including Drosophila, C.elegans, sea urchin, etc.

organism
type: Class
subclass of: assay biology component
definition: The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote.

cellular organisms
type: Class
subclass of: organism
definition: This includes all organisms which are made up of cells, e.g. bacteria, plants and animals.

metazoa
type: Class
subclass of: eukaryote
definition: Metazoa comprises of animals, which are multicellular eukaryotic organisms. This includes those having a vertebral column (e.g. fish, frog, snake, bird, human) and those that do not (e.g. worm, fly, star fish, etc).

assay biology component
type: Class

scRNAseq_2019_Avalos
type: NamedIndividual
type: project
type: Restriction
  on property: is_specified_output_of
  some values from: single-cell RNA-Seq
filtered gene count: 36488
total gene count: 82212
node label: DataSet
definition: Single-cell RNA-seq study of first instar larval brains upon starvation
licence: VFBlicense CC BY 4 0
references: FBrf0244302
database_cross_reference: scExpressionAtlas

Axiom
annotated source: scRNAseq_2019_Avalos
annotated property: database_cross_reference
annotated target: scExpressionAtlas
accession: E-GEOD-134722

scRNAseq_2019_Avalos_FED
type: NamedIndividual
type: biosample
type: Restriction
  on property: overlaps
  some values from: larval brain
type: Restriction
  on property: existence overlaps
  some values from: first instar larval stage
input of: scRNAseq_2019_Avalos_FED_seq
node label: Sample
definition: Cells from first instar larval brain upon normal feeding condition
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq
type: NamedIndividual
type: assay
type: Restriction
  on property: has assay method
  some values from: 10x sequencing
has input: scRNAseq_2019_Avalos_FED
node label: Assay
definition: Single-cell RNA-seq of cells from first instar larval brain upon normal feeding condition
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering
type: NamedIndividual
type: cell clustering analysis
has part: scRNAseq_2019_Avalos_FED
has part: scRNAseq_2019_Avalos_FED_seq
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_neurons
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: larval neuron
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 16
filtered gene count: 1563
total gene count: 5733
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, neurons cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_peptidergic_neurons
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: larval peptidergic neuron
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 290
filtered gene count: 4474
total gene count: 9580
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, peptidergic neurons cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_cholinergic_neurons
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: larval cholinergic neuron
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 383
filtered gene count: 3222
total gene count: 9230
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, cholinergic neurons cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_glial_cells
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: larval glial cell
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 69
filtered gene count: 4608
total gene count: 8856
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, glial cells cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_neuroblasts
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: neuroblast
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 300
filtered gene count: 4589
total gene count: 9588
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, neuroblasts cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_Kenyon_cells
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: larval Kenyon cell
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 29
filtered gene count: 2113
total gene count: 6197
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, Kenyon cells cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_optic_lobe_neuroepithelial_cells
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: optic lobe neuroepithelial cell
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 47
filtered gene count: 5328
total gene count: 8500
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, optic lobe neuroepithelial cells cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_glutamatergic_neurons
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: larval glutamatergic neuron
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 126
filtered gene count: 2782
total gene count: 8184
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, glutamatergic neurons cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_GABAergic_neurons
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: larval GABAergic neuron
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 113
filtered gene count: 3984
total gene count: 8486
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, GABAergic neurons cluster
source: scRNAseq_2019_Avalos

scRNAseq_2019_Avalos_FED_seq_clustering_aminergic_neurons
type: NamedIndividual
type: transcriptional cell cluster
type: Restriction
  on property: composed primarily of
  some values from: larval aminergic neuron
type: Restriction
  on property: existence overlaps
  some values from: larval stage
part of: scRNAseq_2019_Avalos_FED_seq_clustering
cell count: 51
filtered gene count: 3825
total gene count: 7858
node label: Cluster
definition: Clustering analysis of cells from first instar larval brain upon normal feeding condition, aminergic neurons cluster
source: scRNAseq_2019_Avalos

FBrf0244302
type: NamedIndividual
node label: pub