An ontology of Drosophila melanogaster scRNAseq data from a single dataset (FBlc0006404). This information is taken from FlyBase, which sources it from the EMBL-EBI Single Cell Expression Atlas, which compiles scRNAseq data from multiple sources.
VFB scRNAseq Ontology for dataset FBlc0006404
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.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
PERSON:Daniel Schober
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
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.
is a defining property chain axiom where second argument is reflexive
disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
Reference database or publication source.
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
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'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
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
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])
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
A relation between a developmental stage and another, larger developmental stage during which it happens.
Creating this relation as a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO.
see is_input_of example_of_usage
The inverse property of is specified input of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
has specified input
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
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
is specified input of
The inverse property of is specified output of
has specified output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is specified output of
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
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.
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
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.
inheres_in
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.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
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).
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).
A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.
concretizes
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
is role of
role_of
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.
role of
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
has_role
has role
A relation that holds between two neurons that are electrically coupled via gap junctions.
relation between an anatomical structure and a neuron projection bundle that has synaptic terminals in the structure.
innervated by
has synaptic terminal of
A part of relation that applies only between occurrents.
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
Relation between a neuron and a material anatomical entity that its soma is part of.
<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)
has soma location
relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
(forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
fasciculates with
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
synapsed by
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapsed in
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))
has postsynaptic terminal in
synapses in
<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?)
has presynaptic terminal in
Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
synapsed to
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.
<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?)
has synaptic terminal in
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
has fasciculating component
(forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
has fasciculating neuron projection
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<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?)))
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
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)
continuous with
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
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
This is the transitive form of the develops from relation
develops from
develops into
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
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
expressed in
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
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.
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)".
capable of
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.
capable of part of
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
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.
has input
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
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
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
developmentally succeeded by
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.
expresses
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.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
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.
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
genomically related to
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
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).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted.
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
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.
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 yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
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.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
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.
This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
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.
relation between physical entity and a process or stage
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))
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.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
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.
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
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
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.
causal relation between material entity and a process
Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
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*.
Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
is carrier of
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.
has synaptic IO in region
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
receives synaptic input in region
A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
sends synaptic output to region
A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.
receives synaptic input from neuron
A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.
Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron.
sends synaptic output to cell
An optic lobe intrinsic neuron has its synapses restricted to optic lobe neuropil.
A relationship between a neuron and a region, where all of the functionally relevant input and output synapses are in that region.
This relation may still be used if a very small number of synapses fall slightly outside the boundaries of the region, but any class using this relation should not have another restriction using this relation to another non-overlapping region.
synapses restricted to region
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
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.
See github ticket https://github.com/oborel/obo-relations/issues/497
device utilizes material
This property only applies to anatomical entities.
Any anatomical entity (FBbt:10000000) that develops from some germ layer (FBbt:00000110).
An individual member of the species Drosophila melanogaster.
One of the three main divisions of the whole organism formed from groups of segments.
One of the repeated divisions of the whole organism.
Anterior part of the organism, including mouthparts, some sensory structures and the brain.
Head segment derived from the second embryonic segment (between the labral and antennal segments). In the larva, this segment includes Bolwig's organ.
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.
Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).
A segment that is anterior to the gnathal segments.
Anteriormost procephalic segment, anterior to the ocular segment. In the adult it bears the clypeo-labrum.
Segment anterior to the intercalary segment. In the adult it bears the antennae.
Most posterior of the procephalic segments. Contains the tritocerebrum.
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).
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).
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).
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).
The region of the ectoderm anterior to the cephalic furrow.
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.
Primordium of the late extended germ band and closure embryo that gives rise to the larval inner optic anlage. It develops from the anterior lip of the visual primordium.
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.
The sum of all the structures in the embryo that will develop into the embryonic/larval nervous system.
presumptive embryonic/larval nervous system
The sum of all the structures in the embryo that will develop into the embryonic/larval central nervous system.
presumptive embryonic/larval central nervous system
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).
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.
Primordium that develops from the posterior procephalic region of the embryo and gives rise to visual structures of the larva and adult (Green et al., 1993; Chang et al., 2001). An optic placode forms from cells of the visual primordium when they become columnar in shape towards the end of stage 11 (Green et al., 1993; Chang et al., 2001). This placode invaginates during stages 12-13, forming a deep pouch of approximately 85 cells (Green et al., 1993). Its ventral lip segregates from the rest of the primordium and develops into the Bolwig organ (Green et al., 1993). The remainder of the placode, which will form the optic lobe, detaches from the surface of the embryo and attaches to the lateral brain, maintaining a tubular appearance until larval hatching (Green et al., 1993). Its anterior and posterior domains will become the larval inner and outer optic anlage, respectively (Chang et al., 2001). The cells that will become the eye disc are anterior and dorsal to the optic lobe placode cells (Chang et al., 2001). They move into the interior of the embryo during head involution, when they are pushed under the dorsal ridge (Huang et al., 2017).
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).
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.
An equivalence group of the neurectoderm where all cells can, although only one will, become a neural progenitor cell.
Precursor cell that can give rise to all the neuronal and support cells that form a peripheral sense organ.
Glial cell of the central nervous system.
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.
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.
Glial cell located amongst neuronal cell bodies in the cell body rind of the embryonic/larval central nervous system.
Glial cell of the CNS that is associated with neuropil compartments, including synaptic and tract neuropil (Hartenstein, 2011; Omoto et al., 2015; Kremer et al., 2017). These cells have their cell bodies located in the neuropil glial sheath, between the neuropil and the cell body rind, and many of them extend processes into the neuropil (Hartenstein, 2011; Omoto et al., 2015). Two subtypes have been identified, the reticular (astrocyte-like) and ensheathing glia (Hartenstein, 2011; Omoto et al., 2015), which both function in ionic and neurotransmitter homeostasis (Kremer et al., 2017).
Glial cell that is part of the peripheral nervous system.
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).
A neuroblast located in the protocerebrum. None of these are serial homologues of neuroblasts found in the thoracic neuromeres (Urbach et al., 2016).
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).
A neuroblast located in the deutocerebrum. Some of these are serial homologues of neuroblasts found in the thoracic neuromeres (Urbach et al., 2016).
A neuroblast located in the tritocerebrum. Most, if not all, of these have serial homology to neuroblasts found in the thoracic neuromeres (Urbach et al., 2016). There are 13 of these, of which four produce a secondary lineage (Kuert et al., 2012; Urbach et al., 2016).
Any neuron (FBbt:00005106) that has its soma located in some supraesophageal ganglion (FBbt:00003626).
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).
This includes immature secondary neurons that are found in the larva - https://orcid.org/0000-0002-1373-1705.
Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993).
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).
Primordium from which the eye-antennal disc develops.
Organism during the period between hatching and prepupa formation.
Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis.
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.
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).
Figure 12 from Cohen (1993, Bate, Martinez Arias, 1993: 747--841) provides a fate map of the eye-antennal disc.
Anterior, bulbous portion of the eye-antennal disc that gives rise to the eye as well as contributing to the head capsule (Cohen, 1993).
A cluster of cells in the eye-disc that is the precursor to an adult ommatidium. Eventually there are approximately 750 ommatidial precursor clusters per eye-disc, the first forming at approximately 70hrs before pupation along the morphogenic furrow. A new row of adult ommatidial precursors then emerges from the morphogenic furrow roughly every 1.5 hours.
Central nervous system of the embryo/larva.
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).
embryonic/larval supraesophageal complex
embryonic/larval supraesophageal ganglion
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.
The lateral, outer layer of the larval optic lobe. It consists of neuroepithelial cells (and later of proliferating neuroblasts) that will give rise to the neurons of the adult lamina and outer medulla. By the late first instar, it is dome shaped and perforated at its center by a pore, through which axons of the optic stalk pass (Meinertzhagen and Hanson, 1993). Some of these axons form synapses in the larval optic neuropil, which is largely within this pore (Sprecher et al., 2011). It becomes distinguished from the inner optic anlage during the second half of the first instar period (Meinertzhagen and Hanson, 1993). In the third instar, neuroepithelial cells in the medial region give rise to neuroblasts that divide asymmetrically to generate the adult optic lobe neurons. This anlage is patterned by expression of Optix and Vsx1 in complementary regions (Gold and Brand, 2014).
'proliferation center' synonyms usually used for later stages of development (Ngo et al., 2017 - FBrf0236058).
A(n) anlage that develops into some medulla. It develops from some larval optic anlage.
A neuroblast that is the precursor of the medulla. The neuroblasts that give rise to the outer medulla neurons are located in the medial edge of the larval outer optic anlage, whereas the neuroblasts that give rise to the inner medulla neurons are located in the larval inner optic anlage.
Can be distinguished from other optic lobe neuroblasts based on expression of dpn and ase (Konstantinides et al., 2022).
A zone of proliferating neuroblasts that forms at mid third instar, at the lateral rim of the outer optic anlage. Descendants of these neuroblasts form the adult lamina.
A neuroblast that is the precursor of the lamina. The neuroblasts that give rise to the lamina neurons are located in the lateral edge of the larval outer optic anlage.
Anlage of the embryo/larva that is the precursor to the adult lobula.
A(n) anlage that develops into some lobula plate. It develops from some larval inner optic anlage.
Region of the adult brain cell body rind that overlies the lobula plate.
A ribbon-like layer of neuroepithelial cells (and later of proliferating neuroblasts) in the larval optic lobe that gives rise to the adult inner medulla, lobula and lobula plate neurons. In early larval stages it is composed of neuroepithelial cells that divide symmetrically. In the early second instar it becomes U shaped, with the opening of the U pointing in a dorso-caudal direction. It becomes distinguished from the outer optic anlage during the second half of the first instar period (Meinertzhagen and Hanson, 1993). In the third instar, neuroepithelial cells in the medial region give rise to neuroblasts that divide asymmetrically to generate the adult optic lobe neurons.
Tritocerebrum of the late embryonic or larval brain. It is found at the base of the brain hemispheres, partially below the esophagus (Hartenstein et al., 2015; Hartenstein et al., 2018).
larval anterior periesophageal neuropils
Nerve that innervates the supraesophageal ganglion.
Any neuron (FBbt:00005106) that has its soma located in some subesophageal zone (FBbt:00051068).
Any larval sense organ (FBbt:00002639) that is part of some ocular segment (FBbt:00000005).
embryonic/larval ocular segment sensillum
Any larval sense organ (FBbt:00002639) that is part of some labral segment (FBbt:00000008).
embryonic/larval labral segment sense organ
Any larval sense organ (FBbt:00002639) that is part of some antennal segment (FBbt:00000009).
embryonic/larval antennal segment sensillum
Any sense organ (FBbt:00005155) that is part of some intercalary segment (FBbt:00000010).
The prepupa is the name given to the organism at the period of the life cycle that 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 is approximately 12 hours. It occurs 120-132.2 hours after egg laying, and is the period of 0-12.2 hours after puparium formation.
The pupa is the name given to the organism at the period of the life cycle that begins 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. The duration of this stage is approximately 32 hours at 25 degrees C, and spans from 132.2-164.3 hours after egg laying, or is the period of 12.2-44.3 hours after puparium formation.
Organism at any stage after completing eclosion.
Digestive system of the adult, comprising the alimentary canal, mouthparts, labellar glands, salivary glands and Malpighian tubules (Miller, 1950). The adult alimentary canal and salivary glands arise anew from precursors during metamorphosis (Bodenstein, 1950). The adult Malpighian tubules are remodelled from those of the larva (Bodenstein, 1950).
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.
Portion of the adult central nervous system found in the head, consisting of the cerebral and gnathal ganglia (Ito et al., 2014).
Superficial layer of the brain, composed of glia and the cell bodies of neurons (soma).
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.
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.
In the adult, this region is referred to as cerebral ganglia (Ito et al., 2014).
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).
Urbach and Technau (2003) divide the protocerebrum into labral and ocular neuromeres.
A region of the adult brain that processes visual information from the compound eyes.
Neuron that has its cell body in the adult optic lobe. These neurons develop from neuroblasts of the larval optic anlage (Hofbauer and Campos-Ortega, 1990).
Lateral-most synaptic neuropil domain of the adult optic lobes, lying just beneath the compound eyes. It is composed of an array of repetitive cartridge-like units, each of which receives axons from specific sets of ommatidia in the compound eyes.
Monopolar, intrinsic unicolumnar neuron of the adult optic lobe that has its soma in the cell body rind of the lamina and connects the lamina to the medulla (Fischbach and Dittrich, 1989). It has a single major projection that projects along one optic cartridge in the lamina, crosses the first optic chiasm and terminates in the same cartridge in the medulla (Fischbach and Dittrich, 1989).
Lamina monopolar neuron that has short collaterals projecting radially from the main projection in the lamina and arborization in medulla layers M1 and M5 (Fischbach and Dittrich, 1989; Kind et al., 2021). In the lamina, these short collaterals are strongly postsynaptic to the terminals of photoreceptors R1-6 (Rivera-Alba et al., 2011). In the medulla, it makes strong reciprocal synaptic connections with lamina monopolar cell L5 and centrifugal neuron C2, as well as substantial output synapses to C3, Mi1 and Tm3 cells (Takemura et al., 2013). It is also electrically synapsed to lamina monopolar neuron L2 (Joesch et al., 2010). It is a glutamatergic neuron (Gao et al., 2008; Takemura et al., 2011). There is usually one of these cells per optic column (Nern et al., 2025).
The neurotransmitter was assessed by labelling cells with a vGlut[OK371]-dVP16AD-GAL4 driver (FBti0129742) (Gao et al., 2008) or by single cell RT-PCR with specific primers (Takemura et al., 2011). Cell connectivity in the lamina was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for L1 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: R1 (-/40), R2 (-/43), R3 (-/37), R4 (-/38), R5 (-/38), R6 (-/45), L2 (-/3), Lai (-/1), C3 (-/3) and Lawf (-/1) (Rivera-Alba et al., 2011). Connectivity in the medulla was extrapolated from serial EM of 7 columns from a single sample (Takemura et al., 2013). Electrical connectivity was shown by dye labelling (Joesch et al., 2010).
A lamina monopolar neuron with short collaterals that project radially from the main projection in the lamina and that arborizes in medulla layer M2. In the lamina it receives strong input from photoreceptors R1-R6 (Rivera-Alba et al., 2011). It has both pre- and postsynaptic connections in medulla layer M2, with strong synaptic input coming from centrifugal neurons C2 and C3 (Takemura et al., 2013). It has a large number of presynaptic connections to lamina monopolar neuron L5, columnar neuron T1, and transmedullary neurons Tm1, Tm2 and Tm4 (Takemura et al., 2013). It is a cholinergic neuron (Takemura et al., 2011) and is electrically synapsed to lamina monopolar neuron L1 (Joesch et al., 2010). There is usually one of these cells per optic column (Nern et al., 2025).
Cell connectivity in the lamina was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for L2 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: R1 (1/46), R2 (1/45), R3 (-/39), R4 (-/41), R5 (-/39), R6 (-/47), L1 (3/-), L4 (10/7), L5 (1/-), Lai (-/1), C2 (-/3), C3 (-/5) and Lwf (-/7) (Rivera-Alba et al., 2011). Connectivity in the medulla was extrapolated from serial EM of 7 columns from a single sample (Takemura et al., 2013). Note that for many of the output synapses in M2, Tm1 and Tm2 share the same sites (Takemura et al., 2008; Takemura et al., 2011). Electrical connectivity was shown by dye labelling (Joesch et al., 2010). The neurotransmitter was assessed by single cell RT-PCR measurement of choline acetyltransferase (FBgn0000303) expression (Takemura et al., 2011).
Lamina monopolar neuron with short spines that project to one side of the main projection as it extends through the lamina (Fischbach and Dittrich, 1989; Kind et al., 2021). It terminates with an arborization in medulla layer M3 (Fischbach and Dittrich, 1989; Kind et al., 2021). In the lamina it is postsynaptic to the outer photoreceptors (R1-R6) (Rivera-Alba et al., 2011). It also receives input from the inner photoreceptors, partly in the first optic chiasm and partly in the medulla (Kind et al., 2021). It forms presynaptic terminals in medulla layer M3 (Takemura et al., 2008), with strong outputs to Mi9 and Tm20 (Takemura et al., 2013). It is a GABAergic neuron (Raghu et al., 2013). There is usually one of these cells per optic column (Nern et al., 2025).
Cell connectivity in the lamina was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for L3 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: R1 (-/11), R2 (-/10), R3 (-/4), R4 (-/8), R5 (-/6), R6 (-/12), L4 (-/1), L5 (1/-), Lai (-/10) and Lawf (-/17) (Rivera-Alba et al., 2011). Connectivity in the medulla was extrapolated from serial EM of 3 columns from a single sample (Takemura et al., 2008) or from 7 columns (Takemura et al., 2013). The neurotransmitter was assessed by the intersection of the expression of the VGAT-GAL4 driver (FBtp0069181) and an antibody against GABA (Raghu et al., 2013).
A lamina monopolar neuron that arborizes in the proximal lamina, forms a spreading arbor in medulla layer M2 and a small terminal arbor in M4-M5 that penetrates adjacent columns (Fischbach and Dittrich, 1989; Takemura et al., 2008; Takemura et al., 2011). In the medulla it forms presynaptic terminals in both M2 and M4-M5 with transmedullary neuron Tm2; three L4 neurons, one from the parent column and two from the posterior ones contact the same Tm2 neuron (Takemura et al., 2008; Takemura et al., 2011). It seems to be capable of both cholinergic and GABAergic neurotransmission.
Note, Fischbach and Dittrich (1989) have this as arborizing in M4, but we follow the more detailed analysis of Takemura and colleagues (2008) who place the terminal arbor in M5. This difference may have to do with the different ways the two papers define L4. Note also that L4x and L4y are simply a way of referring to L4 collaterals from an adjacent cartridge in descriptions of synaptic connectivity (see Meinertzhagen and O'Neil, 1991) and are not separate neurons. Connectivity in the medulla was extrapolated from serial EM of 3 columns from a single sample (Takemura et al., 2008; Takemura et al., 2011). Takemura et al. (2011) and Davis et al. (2020) report the neurotransmitter to be acetylcholine as assessed by single cell RT-PCR measurement of choline acetyltransferase (FBgn0000303) expression and scRNAseq detection of both choline acetyltransferase and vesicular acetylcholine transporter (FBgn0270928). However, Raghu et al. (2013) report this neuron to be GABAergic as assessed by the intersection of the expression of the VGAT-GAL4 driver (FBtp0069181) and an antibody against GABA.
A lamina monopolar neuron that hardly arborizes at all in the lamina, but forms a branched arborization in medulla layers M1 and M2 and a clump of terminals in M5. In the medulla, it forms strong reciprocal synaptic connections with monopolar lamina monopolar neuron L1 (Takemura et al., 2013). It also receives substantial input from L2 and C2 neurons and has many presynapses connecting to medullary intrinsic neurons Mi1 and Mi4, and to transmedullary neuron Tm3a (Takemura et al., 2013). It is a cholinergic neuron (Davis et al., 2020). There is usually one of these cells per optic column (Nern et al., 2025).
Pre- versus postsynaptic innervation judged by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. Connectivity in the medulla was extrapolated from serial EM of 7 columns from a single sample (Takemura et al., 2013).
Intrinsic columnar neuron of the optic lobe that has its cell body in the posterior part of the optic lobe and a cell body fiber that bifurcates in the second optic chiasma (Fischbach and Dittrich, 1989). It has two branches, each targeting a different neuropil adjacent to the second optic chiasma (lobula, lobula plate and medulla) (Fischbach and Dittrich, 1989).
An intrinsic columnar neuron whose cell body lies in the cortex of the medulla. The fiber of the T1 cell body branches at the medulla surface to form a T-shaped linking fiber between a bush-like arborization in the distal part of a medulla column (M1 and M2), and a bundle of climbing fibers in the equivalent column of the lamina (Fischbach and Dittrich, 1989). Synaptic connections in the lamina are exclusively postsynaptic and include a large number of connections from lamina intrinsic (amacrine) neurons (Meinertzhagen and O'Neil, 1991; Rivera-Alba et al., 2011). In the medulla, it is strongly synapsed by centrifugal neuron C3 in medulla layer M2 and lamina monopolar neuron L2 (Takemura et al., 2008; Takemura et al., 2013). There is usually one of these cells per optic column (Nern et al., 2025).
Cell connectivity in the lamina was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for T1 (presynaptic/postsynaptic) in a single lamina cartridge for each cell type was the following: R2 (-/2), R3 (-/2), R4 (-/2), Lai (-/54), C3 (-/1) and Lawf (-/1) (Rivera-Alba et al., 2011). Connectivity in the medulla was extrapolated from serial EM of 3 columns from a single sample (Takemura et al., 2008) or from 7 columns (Takemura et al., 2013).
T neuron with its cell body posterior to the lobula plate and a cell body fiber that projects through the lobula plate and via the second optic chiasma, with little or no arborization, to medulla layer 10 (Fischbach and Dittrich, 1989; Shinomiya et al., 2019). It forms a fine arborization in medulla layers M9 and M10 and its axon then doubles back across the second optic chiasma to form bleb-type arborizations in a single layer of the lobula plate (Fischbach and Dittrich, 1989; Shinomiya et al., 2019). It is a cholinergic neuron (Mauss et al., 2014; Shinomiya et al., 2014). There are a large number of these cells, which are generated from neuroblasts that amplify by symmetric division (type III) before generating the T4 (and T5) neurons (Mora et al., 2018).
Pre- versus postsynaptic innervation judged by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. The neurotransmitter was assessed with a split-GAL4 strategy using a Chat-DBD allele (FBal0198074) (Mauss et al., 2014) and single-cell transcript profiling (Shinomiya et al., 2014).
T neuron with its cell body in the lobula plate cell body rind and a cell body fiber that projects through the lobula plate and via the second optic chiasma, with little or no arborization, to lobula layer 1 (Fischbach and Dittrich, 1989; Shinomiya et al., 2019). It forms a fine arborization in lobula layer 1, then its axon doubles back across the second optic chiasma to form bleb-type arborizations in a single layer of the lobula plate (Fischbach and Dittrich, 1989; Shinomiya et al., 2019). It is a cholinergic neuron (Mauss et al., 2014; Shinomiya et al., 2014). There are a large number of these cells, which are generated from neuroblasts that amplify by symmetric division (type III) before generating the T5 (and T4) neurons (Mora et al., 2018).
Pre- versus postsynaptic innervation judged by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. The neurotransmitter was assessed with a split-GAL4 strategy using a Chat-DBD allele (FBal0198074) (Mauss et al., 2014) and single-cell transcript profiling (Shinomiya et al., 2014). Connectivity in the lobula was assessed by serial section electron microscopy of a single column (Shinomiya et al., 2014).
A lamina wide-field neuron that has a main projection that ascends via the first optic chiasm into the lamina where it is restricted to a single column for most of its length before making wide-field arborizations in the distal lamina. These neurons also arborize on the distal surface of the medulla in a circular field of about 20 columns. Several linking fibers from this arborization descend into M4 where they form a wide arborization field covering about 30-40 columns (Fischbach and Dittrich, 1989; Morante and Desplan, 2008). In the lamina, it forms numerous presynaptic connections to lamina monopolar neuron L3 and lamina intrinsic (amacrine) neuron (Rivera-Alba et al., 2011).
Pre-synaptic terminals were assessed by labelling with a UAS-Synaptotagmin reporter (P{UAS-HA-syt} - FBtp0015803). The identification of dendrites and axons was done using a UAS-Dscam (P{UAS-Dscam.exon17.1.GFP} - FBtp0021447) or a UAS-tau (P{UAS-tau-lacZ.O} - FBtp0010033) reporter, respectively (Morante and Desplan, 2008). Cell connectivity in the lamina was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for Lawf (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: R1 (1/1), R2 (3/-), R3 (1/-), R6 (1/-), L1 (1/-), L2 (7/-), L3 (17/-), L5 (1/-), Lai (24/-), T1 (1/-), C2 (3/-), C3 (2/-), Lawf collaterals (5) and epithelial glia (6/-) (Rivera-Alba et al., 2011).
Columnar neuron whose soma lies in the cortex between the medulla and the lobula plate that extends through a single column of the medulla and lamina.
Adult centrifugal neuron with arborizations in the medulla layers M1, M5/M6, M8 and M10 and more restricted arborizations in the lamina (Fischbach and Dittrich, 1989; Kind et al., 2021). In the medulla, it makes reciprocal connections to lamina monopolar neuron L1, and is presynaptic to L2 and L5, as well as medullary intrinsic neuron Mi1 (Takemura et al., 2013). It is GABAergic (Fei et al., 2010). There is usually one of these cells per optic column (Nern et al., 2025).
Pre- versus postsynaptic innervation in the proximal medulla was inferred by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. Connectivity in the medulla was extrapolated from serial EM of 7 columns from a single sample (Takemura et al., 2013).
Adult centrifugal neuron with arborizations in medulla layers M1-2, M5, and M9-10 and more restricted arborizations in the lamina (Fischbach and Dittrich, 1989; Kind et al., 2021). It forms presynapses and postsynapses in the lamina (Morante and Desplan, 2008; Rivera-Alba et al., 2011). In the medulla it is strongly presynaptic to monopolar lamina neuron L2 and columnar neuron T1, and strongly postsynaptic to L1 (Takemura et al., 2013). It is GABAergic (Fei et al., 2010). There is usually one of these cells per optic column (Nern et al., 2025).
Pre-synaptic terminals were assessed by labelling with a UAS-Synaptotagmin reporter (P{UAS-HA-syt} - FBtp0015803). The identification of dendrites was done using a UAS-Dscam (P{UAS-Dscam.exon17.1.GFP} - FBtp0021447) reporter (Morante and Desplan, 2008). Cell connectivity in the lamina was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. Connectivity in the medulla was extrapolated from serial EM of 7 columns from a single sample (Takemura et al., 2013).
Tangential neuron of the optic lobe that projects and arborizes along the plane of one or more layers of the lamina.
Intrinsic amacrine neuron of the lamina with arborizations spanning the proximal and distal lamina, whose cell body lies proximal to the lamina (Fischbach and Dittrich, 1989; Meinertzhagen and Sorra, 2001). It has extensive arborizations and forms a substantial number of presynaptic terminals with columnar neuron T1 and epithelial glia (Rivera-Alba et al., 2011). It receives strong input from each of photoreceptors R1-R6, and from lamina wide-field cells (Rivera-Alba et al., 2011). It is a glutamatergic neuron (Davis et al., 2020). There are approximately 210 of these cells on each side (Nern et al., 2025).
Cell connectivity in the lamina was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for Lai (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: R1 (-/36), R2 (1/39), R3 (-/39), R4 (2/37), R5 (2/35), R6 (-/40), L1 (1/-), L2 (1/-), L3 (10/-), L4 (4/2), L5 (4/-), Lai (1), T1 (54/1), C2 (1/5), C3 (1/9), Lawf (-/24) and epithelial glia (87/-) (Rivera-Alba et al., 2011).
Segment (column) of the lamina defined by the distal-proximal (eye to central brain) projections of photoreceptor cells of a single ommatidium.
The second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla (Ito et al., 2014).
Nern et al. (2025) - FBrf0262545 say distal is M1-5 and M6-7 is central medulla.
Distal-most layer of the medulla. It is defined by the distal extent of the distal lamina monopolar neuron L1 arborization (Fischbach and Dittrich, 1989).
In the literature there are two methods for describing spatial location of neurons in the visual system: distal-proximal (e.g. Fischbach and Dittrich, 1989), and medial-lateral (e.g. Ito et al., 2014), both meaning outer and inner, and refer to the distance of a structure along the visual pathway relative to the center of the brain. Currently we will adopt the classical 'distal-proximal'.
Second most lateral layer of the medulla. It is defined by the distal extent of the distal lamina monopolar neuron L2 arborization (Fischbach and Dittrich, 1989).
Third most lateral layer of the medulla. It is defined by the proximal border of the lamina monopolar neuron L2 arborization to that of the lamina neuron L3 terminal (Fischbach and Dittrich, 1989).
Fourth most lateral layer of the medulla. It corresponds to the narrow layer between the proximal end of lamina neuron L3 and the distal border of lamina neuron L1's proximal arborization (Takemura et al., 2008).
In the literature there are two methods for describing spatial location of neurons in the visual system: distal-proximal (e.g. Fischbach and Dittrich, 1989), and medial-lateral (e.g. Ito et al., 2014), both meaning outer and inner, and refer to the distance of a structure along the visual pathway relative to the center of the brain. We use the classical 'distal-proximal'.
Fifth most lateral layer of the medulla. It is defined by the lamina neuron L1's proximal arborization and contains the proximal lamina neuron L5 terminal (Fischbach and Dittrich, 1989).
Sixth most lateral layer of the medulla, immediately lateral to the serpentine layer. It lies between the lamina neuron L1's arborization and the serpentine layer (Fischbach and Dittrich, 1989).
Lateral-most layer of the inner medulla, immediately medial to the serpentine layer.
Inner-most layer of the medulla. Practically it is defined by the height of the T4 neuron terminal arborizations.
An amacrine neuron that is intrinsic to the medulla, whose soma is located in the cortex of the medulla and that branches and arborizes in the distal medulla. These neurons project through the distal surface of the medulla, to form wide (sometimes very wide) terminal arborizations mainly or completely restricted to a single layer of the medulla.
A columnar neuron that is intrinsic to the medulla, connecting distal and proximal layers (Fischbach and Dittrich, 1989; Kind et al., 2021). It has its soma in the cell body rind of the medulla (Fischbach and Dittrich, 1989).
Unicolumnar medullary intrinsic neuron with bushy, fine arborizations in medulla layers M1, M5 and M9-10 (Fischbach and Dittrich, 1989; Kind et al., 2021). The projection of this neuron branches at the inner-face of the medulla to form two to three varicose recurrent terminal specializations that extend back up to the inner border of layer M8 (Fischbach and Dittrich, 1989; Morante and Desplan, 2008). In central (non-dorsal margin) columns it receives input from an R8 photoreceptor cell, but connections are substantially weaker in dorsal margin columns (Kind et al., 2021). Pre-synaptic terminals are present mainly in medulla layers M9-M10, but also in all other layers where neurites extend laterally (Pankova and Borst, 2017). It receives input from lamina monopolar neurons L1 and L5 and centrifugal neuron C2 (Takemura et al., 2013). It outputs to T4 neurons and transmedullary neuron Tm3a (Takemura et al., 2013). It is a cholinergic neuron (Hasegawa et al., 2011; Pankova and Borst, 2017). There is usually one of these cells per optic column (Nern et al., 2025).
small field unilateral tristratified neuron
Pre-synaptic terminals were assessed by labelling with a UAS-Synaptotagmin reporter (P{UAS-HA-syt} - FBtp0015803). The neurotransmitter was assessed by labelling cells with an anti-ChAT antibody (Hasegawa et al., 2011). The morphology of the terminals was judged from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. Connectivity and morphology in the medulla were assessed by electron microscopy reconstruction from 7 columns (Takemura et al., 2013).
Medulla intrinsic narrow field neuron with both fine and bleb-type arborizations in medulla layers M1, M2, M3 and M8, but with only fine arborizations in medulla layers M4 and M5, and only bleb-type arborizations in medulla layer M9 (Morante and Desplan, 2008; Fischbach and Dittrich, 1989). It receives input from the lamina monopolar neuron L5 and photoreceptor R8 (Takemura et al., 2013). It is a GABAergic neuron (Takemura et al., 2017). There is usually one of these cells per optic column (Nern et al., 2025).
Raghu and Borst (2011) identified this as glutamatergic using a vGlut[CNSIII]-GAL4 driver (FBti0129148), but vGlut antibody staining performed by Takemura et al. (2017) was not strong compared to neighboring cells, whereas GAD1 staining was strong. Pre- versus postsynaptic innervation judged by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. Connectivity in the medulla was assessed by electron microscopy reconstruction from 7 columns (Takemura et al., 2013). Kind et al. (2020) say that it is not contacted by R7/R8 in the DRA, but not clear whether Mi4 is present in the DRA.
Medulla intrinsic narrow field neuron with a bushy mix of bleb-type and fine terminal arborization in layers M2, M3 and M4 and in the lower medulla layers M9-M10 (Fischbach and Dittrich, 1989; Kind et al., 2021). It establishes pre- and post-synaptic connections in both the inner and outer medulla layers (Fischbach and Dittrich, 1989; Morante and Desplan, 2008). It receives input from lamina monopolar neuron L3 (Takemura et al., 2013). It is glutamatergic (Takemura et al., 2017). There is usually one of these cells per optic column (Nern et al., 2025).
Pre-synaptic terminals were assessed by labelling with a UAS-Synaptotagmin reporter (P{UAS-HA-syt} - FBtp0015803). The identification of dendrites and axons was done using a UAS-Dscam (P{UAS-Dscam.exon17.1.GFP} - FBtp0021447) or a UAS-tau (P{UAS-tau-lacZ.O} - FBtp0010033) reporter, respectively (Morante and Desplan, 2008). Connectivity in the medulla was extrapolated from serial EM from 7 columns (Takemura et al., 2013).
An intrinsic columnar neuron of the optic lobe whose cell body lies in the distal cortex of the medulla and that projects through the medulla and optic chiasm into the lobula. All neurons arborize in the lobula and most, but not all, in the medulla (Fischbach and Dittrich, 1989).
Transmedullary narrow field neuron that terminates in lobula layer 1 with a bleb-type terminal arborization and that has fine arborizations in medulla layer M2 and bleb-type arborizations in M3 and M9 (Fischbach and Dittrich, 1989; Takemura et al., 2011). In the medulla, it receives strong synaptic input from lamina monopolar neuron L2 (Takemura et al., 2011; Takemura et al., 2013). It outputs onto T5 neurons (Shinomiya et al., 2019). It is a cholinergic neuron (Varija Raghu et al., 2011; Shinomiya et al., 2014). There is usually one of these cells per optic column (Nern et al., 2025).
The neurotransmitter was assessed by co-labelling cells with a P{Cha-GAL4.7.4} driver (FBtp0014830) and an anti-ChAT antibody (Varija Raghu et al., 2011; Shinomiya et al., 2014). Pre- versus postsynaptic innervation judged by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. Connectivity in the medulla was extrapolated from serial EM of 3 columns from a single sample (Takemura et al., 2008) or from 7 columns (Takemura et al., 2013). Connectivity in the lobula was assessed by serial section electron microscopy of a single column (Shinomiya et al., 2014). Connectivity in the entire optic lobe was also assessed by EM (Shinomiya et al., 2019).
Transmedullary narrow field neuron that has its main dendritic arborization in medulla layer M2 (Ting et al., 2014), where it receives input from lamina monopolar neuron L2 (Takemura et al., 2011), and additional postsynaptic terminals in M4-M5, where it receives input from lamina monopolar neuron L4 (Takemura et al., 2011). It has presynaptic terminals in layers M3, M4 and M9 (Fischbach and Dittrich, 1989; Takemura et al., 2011). Its axon follows the posterior edge of its cognate medulla column (Ting et al., 2014), then crosses the second optic chiasma to terminate in lobula layers 1 and 2 (Fischbach and Dittrich, 1989). In layer 1 it outputs to T5 neurons (Shinomiya et al., 2014). It is a cholinergic neuron (Varija Raghu et al., 2011; Gao et al., 2008; Takemura et al., 2011). There is usually one of these cells per optic column (Nern et al., 2025).
The neurotransmitter has been assessed by co-labelling cells with a P{Cha-GAL4.7.4} driver (FBtp0014830) and an anti-ChAT antibody (Varija Raghu et al., 2011), by using a Cha-GAL4.DBD (FBtp002350) (Gao et al., 2008) and by neurotransmitter was assessed by single cell RT-PCR measurement of choline acetyltransferase (FBgn0000303) expression (Takemura et al., 2011). Connectivity in the medulla was extrapolated from serial EM of 3 columns from a single sample (Takemura et al., 2008) or from 7 columns (Takemura et al., 2013). Connectivity in the lobula was assessed by serial section electron microscopy of a single column (Shinomiya et al., 2014).
Transmedullary narrow field neuron that terminates in lobula layers 1 and 4 with bleb-like terminal arborizations. It has fine arborizations in medulla layers M1, M4, and M5, and has bleb-type arborization in medulla layers M1, M4, M9 and M10 (Morante and Desplan, 2008; Fischbach and Dittrich, 1989). Pre-synaptic terminals are present mainly in medulla layers M9-M10, but also in all other layers where neurites extend laterally (Pankova and Borst, 2017). It receives input from lamina monopolar neuron L1 and L5 and medullary intrinsic neuron Mi1 and it outputs to T4 neurons (Takemura et al., 2013). It seems to be capable of both cholinergic (Pankova & Borst, 2017) and GABAergic (Raghu et al., 2013) neurotransmission.
Pre- versus postsynaptic innervation judged by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. The neurotransmitter was assessed to be GABA by the intersection of the expression of the VGAT-GAL4 driver (FBtp0069181) and an antibody against GABA (Raghu et al., 2013). Connectivity in the medulla was assessed by electron microscopy reconstruction from 7 columns (Takemura et al., 2013). Neuron was assessed to be cholinergic based on anti-HA antibody detection of HA-tagged VAChT expression (Pankova & Borst, 2017).
Transmedullary narrow field neuron that terminates in lobula layers 1, 2 and 4 with bleb-type arborizations, and with fine arborizations in layer 3. It displays fine arborizations in medulla layers M2, M3, M4 and M9, and has bleb-type arborizations in layers M2, M4, and M9 (Morante and Desplan, 2008; Fischbach and Dittrich, 1989). In the medulla, receives input from lamina monopolar neuron L2 and centrifugal neuron C3 (Takemura et al., 2013). In lobula layer 1, it outputs to T5 neurons (Shinomiya et al., 2014). It seems to be capable of both cholinergic and GABAergic neurotransmission. There is usually one of these cells per optic column (Nern et al., 2025).
The acetylcholine neurotransmitter was assessed by co-labelling cells with a Cha-GAL4.7.4 driver (FBtp0014830) and an anti-ChAT antibody (Varija Raghu et al., 2011), and by scRNAseq detection of choline acetyltransferase (FBgn0000303) and vesicular acetylcholine transporter (FBgn0270928) expression (Davis et al., 2020). The GABA neurotransmitter was assessed by the intersection of the expression of the VGAT-GAL4 driver (FBtp0069181) and an antibody against GABA (Raghu et al., 2013). Pre- versus postsynaptic innervation judged by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. Connectivity in the medulla was extrapolated from serial EM from 7 columns (Takemura et al., 2013). Connectivity in the lobula was assessed by serial section electron microscopy of a single column (Shinomiya et al., 2014).
Transmedullary neuron that terminates in lobula layer 5 with bleb-type arborizations. It displays fine arborizations in medulla layers M3 and M6 and other, depending on the subtype. It has bleb-type terminals in layers M6 and M8. It has three subtypes.
Pre- versus postsynaptic innervation judged by scoring of terminal morphology from figures in Fischbach and Dittrich (1989) as assessed by FlyBrain Neuron DB. In these figures, the neuron has characteristics of the three Tm5 subtypes.
Transmedullary narrow field neuron that has most of its dendritic arborization in medulla layers M2 and M3, with some extensions into M1, M4 and M5 (Gao et al., 2008; Ting et al., 2014), and presynapses in M3 (Gao et al., 2008). Its axon follows the posterior edge of its cognate medulla column (Ting et al., 2014), then crosses in the second optic chiasma and terminates in lobula layer 1 (Fischbach and Dittrich, 1989; Ting et al., 2014), where it outputs to T5 neurons (Shinomiya et al., 2014). It is a cholinergic neuron (Gao et al., 2008; Shinomiya et al., 2014). It expresses the transcription factor sim (Ozel et al., 2021). There is usually one of these cells per optic column (Nern et al., 2025).
Neurotransmitter was assessed using a cha-GAL4DBD driver (Gao et al., 2008), single-cell transcript profiling and immunohistochemistry (Shinomiya et al., 2014). Connectivity in the lobula was assessed by serial section electron microscopy of a single column (Shinomiya et al., 2014).
Transmedullary neuron that has dendritic arborization in medulla layers M1-M3, as well as presynaptic sites in M8 (Fischbach and Dittrich, 1989; Gao et al., 2008). In the medulla, it spans just one column (Kind et al., 2021), and receives input from lamina monopolar neuron L3 (Takemura et al., 2013) and an R8 photoreceptor (Kind et al., 2021). Its axon follows the anterior edge of its cognate medulla column (Ting et al., 2014), then crosses the second optic chiasma and projects to lobula layer 5 (Fischbach and Dittrich, 1989; Gao et al., 2008). It provides input to the lobula intrinsic neuron Li4 via many synapses (Lin et al., 2016). It is a cholinergic neuron (Gao et al., 2008). There is usually one of these cells per optic column (Nern et al., 2025).
Connectivity in the medulla based on EM (Takemura et al., 2013; Kind et al., 2021). Connectivity in the lobula was assessed by GRASP and double-labeling EM (Lin et al., 2016). Neurotransmitter was assessed using a cha-GAL4DBD driver (Gao et al., 2008).
Tangential neuron of the optic lobe that projects and arborizes along the plane of one or more medulla layers.
Anterior domain of the adult lobula complex. It can be divided into six layers and houses many columnar neurons.
Layer of the lobula that abuts the second optic chiasm. It is defined by the bushy arborizations of the T5 neurons, and by the terminal arborizations of transmedullary neuron Tm1 and Tm9.
Layer of the lobula that is second-most from the second optic chiasm. It is defined by the arborizations of lobula tangential neuron LT5.
Layer of the lobula that is third-most from the second optic chiasm. It contains the arborizations of lobula tangential neuron LT6.
Layer of the lobula that is fourth-most from the second optic chiasm. It contains the terminals of the translobula plate Tlp 2, 3, 4 and 5 neurons.
Fischbach and Dittrich, (1989), comment that lobula layer 4 could potentially be further subdivided based on the stratified arborizations of the Tlp neurons.
Tangential neuron of the optic lobe that projects and arborizes along the plane of one or more layers of the lobula.
An extrinsic columnar neuron that innervates the lobula.
Posterior domain of the adult lobula complex. It is divided into 4 layers and houses many large tangential neurons.
Any interneuron that innervates only the lobula plate (Raghu and Borst, 2011).
The projection of axons between the lamina and medulla (first optic chiasma) or between the medulla and lobula (second optic chiasma). The linear order of axons along each horizontal row of retinotopic cartridges or columns is reversed by the chiasma.
Chiasma lying between the medulla and the lobula/lobula plate of the optic lobe (Ito et al., 2014). Between the medulla and the lobula, neuronal fibers reverse their order, inverting the anterior-posterior axis of the visual field (Ito et al., 2014; Shinomiya et al., 2019). Between the medulla and lobula plate and between the lobula and lobula plate, fibers run in parallel, conserving the axes of the visual field (Shinomiya et al., 2019). Neurons travelling between the medulla and lobula complex form around 25-30 fiber bundles of varying widths, and neurons travelling between the same two neuropil columns do not necessarily fasciculate with the same bundle (Shinomiya et al., 2019). Neurons travelling between the lobula and lobula plate form sheet-like structures, neurons from the medulla bundles also merge into these sheets (Shinomiya et al., 2019). Sheets and bundles are wrapped by glial processes (Shinomiya et al., 2019). Approximately 20,000 neurons pass through each second optic chiasma (Shinomiya et al., 2019).
The lobula lies opposite to the lobula plate, with the columns representing the anterior visual field being furthest from the medulla. For that reason, there is no chiasms between the medulla and lobula plate (Ito et al., 2014).
Neuromere of the antennal segment, located between the protocerebrum and tritocerebrum, connected to antennal nerve trunk (Urbach and Technau, 2003; Ito et al., 2014).
Neuromere of intercalary segment, located between the deutocerebrum and the gnathal ganglion (Urbach and Technau, 2003; Hartenstein et al., 2018).
Neuron of the adult central nervous system that has arborization in the sensory neuropil of the subesophageal zone.
Any sensillum (FBbt:00007152) that is part of some head (FBbt:00000004).
The array of photoreceptors and the cells that support them in a compound eye.
This is a very loosely used term. Definition based on consensus usage in literature.
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).
Any developing material anatomical entity of the embryo.
Sensory neuron that reacts to the presence of light, due to the presence of rhodopsin.
Outer photoreceptor cell of the adult eye whose rhabdomere is located at the right angle vertex of the longer of the two parallel sides of the trapezoid of rhabdomeres in each ommatidium. It has a single axon that projects along a single lamina optic cartridge (Fischbach and Dittrich, 1989; Wolff and Ready, 1993).
The name photoreceptor cell R1 is occasionally, mistakenly assumed to refer to any Rh1 (ninaE) expressing photoreceptor cell. This is incorrect. This term only refers to a type of adult eye photoreceptor cell. The name is based simply on the position of the rhabdomere within each ommatidium - see figure 4 in Wolff and Ready, 1993. Cell connectivity was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for R1 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: L1 (40/-), L2 (46/1), L3 (11/-), L4 (-/2), Lai (36/-), Lawf (1/1), epithelial glia (15/-), surface glia (1/-) and marginal glia (1/-) (Rivera-Alba et al., 2011).
Outer photoreceptor cell of the adult eye whose rhabdomere is located in the middle of the longer of the two parallel sides of the trapezoid of rhabdomeres in each ommatidium. It has a single axon that projects along a single lamina optic cartridge (Fischbach and Dittrich, 1989; Wolff and Ready, 1993).
The name photoreceptor cell R2 is occasionally, mistakenly assumed to refer to any Rh2 expressing photoreceptor cell. This is incorrect. This term only refers to a type of adult eye photoreceptor cell. The name is based simply on the position of the cell and its rhabdomere within each ommatidium - see figure 4 in Wolff and Ready, 1993. Cell connectivity was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for R2 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: L1 (43/-), L2 (45/1), L3 (10/-), L4 (-/1), Lai (39/-), T1 (2/-), Lawf (-/3), epithelial glia (13/-) and surface glia (1/-) (Rivera-Alba et al., 2011).
Outer photoreceptor cell of the adult eye whose rhabdomere is located at the non-right angled vertex of the longer of two parallel sides of the trapezoid of rhabdomeres in each ommatidium. It has a single axon that projects along a single lamina optic cartridge (Fischbach and Dittrich, 1989; Wolff and Ready, 1993).
The name photoreceptor cell R3 is occasionally, mistakenly assumed to refer to any Rh3 expressing photoreceptor cell. This is incorrect. This term only refers to a type of adult eye photoreceptor cell. The name is based simply on the position of the cell and its rhabdomere within each ommatidium - see figure 4 in Wolff and Ready, 1993. Cell connectivity was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for R3 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: L1 (37/-), L2 (39/-), L3 (4/-), L4 (-/3), Lai (39/-), T1 (2/-), C3 (2/1), Lawf (-/1) and epithelial glia (7/-) (Rivera-Alba et al., 2011).
Outer photoreceptor cell of the adult eye whose rhabdomere is located in the middle of the longer of the two non-parallel sides of trapezoid of rhabdomeres in each ommatidium, in between the rhabdomeres of R3 and R5. It has a single axon that projects along a single lamina optic cartridge (Fischbach and Dittrich, 1989; Wolff and Ready, 1993).
The name photoreceptor cell R4 is occasionally, mistakenly assumed to refer to any Rh4 expressing photoreceptor cell. This is incorrect. This term only refers to a type of adult eye photoreceptor cell. The name is based simply on the position of the cell and its rhabdomere within each ommatidium - see figure 4 in Wolff and Ready, 1993. Cell connectivity was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for R4 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: L1 (38/-), L2 (41/-), L3 (8/-), L4 (-/1), Lai (37/2), T1 (2/-) and epithelial glia (9/-) (Rivera-Alba et al., 2011).
Outer photoreceptor cell of the adult eye whose rhabdomere is located at a non-right angle vertex of the shorter of the two parallel sides of the trapezoid of rhabdomeres in each ommatidium. It has a single axon that projects along a single lamina optic cartridge (Fischbach and Dittrich, 1989; Wolff and Ready, 1993).
The name photoreceptor cell R5 is occasionally, mistakenly assumed to refer to any Rh5 expressing photoreceptor cell. This is incorrect. This term only refers to a type of adult eye photoreceptor cell. The name is based simply on the position of the cell and its rhabdomere within each ommatidium - see figure 4 in Wolff and Ready, 1993. Cell connectivity was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for R5 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: L1 (38/-), L2 (39/-), L3 (6/-), L4 (-/3), Lai (35/2), C2 (1/-), epithelial glia (10/-) and marginal glia (1/-) (Rivera-Alba et al., 2011).
Outer photoreceptor cell of the adult eye whose rhabdomere is located at the right angle vertex of the shorter of the two parallel sides of the trapezoid of rhabdomeres in each ommatidium. It has a single axon that projects along a single lamina optic cartridge (Fischbach and Dittrich, 1989; Wolff and Ready, 1993).
The name photoreceptor cell R6 is occasionally, mistakenly assumed to refer to any Rh6 expressing photoreceptor cell. This is incorrect. This term only refers to a type of adult eye photoreceptor cell. The name is based simply on the position of the cell and its rhabdomere within each ommatidium - see figure 4 in Wolff and Ready, 1993. Cell connectivity was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for R6 (presynaptic/postsynaptic) in a single lamina cartridge with each cell type was the following: L1 (45/-), L2 (47/-), L3 (12/-), L4 (-/3), Lai (40/-), Lawf (-/1), epithelial glia (11/-) and marginal glia (2/-)(Rivera-Alba et al., 2011).
Inner photoreceptor cell of the ommatidium whose rhabdomere is located distally, directly above that of R8 (Wernet and Desplan, 2004). It has a single axon that extends through a single column of the lamina without making synapses (Fischbach and Dittrich, 1989). This axon crosses the first optic chiasm and extends through a single column of the medulla where it makes pre-synaptic contacts, mainly in medulla layers M1 and M5 (Takemura et al., 2008), before terminating in M6 (Gao et al., 2008; Sancer et al., 2019). It forms reciprocal inhibitory histaminergic synapses with the R8 photoreceptor of the same optic column (Schnaitmann et al., 2018), with a large proportion in the first optic chiasm (Kind et al., 2021).
This term refers to a type of adult eye photoreceptor cell, defined based on the position of its rhabdomere within each ommatidium - see figure 4 in Wolff and Ready (1993). It does not refer to Rh7-expressing photoreceptors.
Inner photoreceptor cell of the ommatidium whose rhabdomere is located proximally, directly below that of R7 (Wernet and Desplan, 2004). It has a single axon that extends through a single column of the lamina without making synapses and crosses the first optic chiasm to reach the medulla (Fischbach and Dittrich, 1989). It forms reciprocal inhibitory histaminergic synapses with the R8 photoreceptor of the same optic column (Schnaitmann et al., 2018), with a large proportion in the first optic chiasm (Kind et al., 2021). It is also cholinergic (Davis et al., 2020).
Fischbach and Dittrich (1989) suggest there may be two (non-DRA) variants of R8, one terminating in each of M3 and M4; this has not been substantiated in subsequent papers.
A bilaterally paired compound sense organ of the adult head that functions in visual perception.
One of the facets of the compound eye. It is composed of eight light-sensing photoreceptor cells (photoreceptor cell R1-R8) and accessory cells. There are around 800 ommatidia in each compound eye.
A division of the whole organism into specialized systems.
The organ system that forms the covering layer of the animal.
The outer non-living layer of the integumentary system that is secreted by the underlying epidermis.
Non-innervated projection of the cuticle around an actin-rich cellular process of an underlying epidermal cell.
Tissue composed of epithelial cells. It secretes and underlies the cuticle.
Organ system comprising the alimentary canal and its associated organs, including the mouthparts, labellar and salivary glands and the Malpighian tubules (Miller, 1950).
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.
All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.
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.
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).
The outer parts of the nervous system that perform sensory and motor functions.
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A neuron projection bundle linking two or more synaptic neuropil domains or subdomains within the CNS.
A bundle of axons connecting the peripheral nervous system to the central nervous system.
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.
Any neuron (FBbt:00005106) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
A neuron that is entirely confined to the central nervous system and is neither a sensory neuron nor a motor neuron.
alt_id of FBbt:00005126 moved over following obsoletion of 'intrinsic neuron', unclear what this term was or whether 'interneuron' is a suitable replacement.
Optic lobe intrinsic neuron without defined axons or dendrites, having processes with mixed pre- and post-synapses in approximately the same ratio throughout the cell (Matsliah et al., 2024). Some amacrine cells, such as CT1, have multiple compartmentalized, modular arborizations (Meier and Borst, 2019).
Interneuron of the optic lobe whose primary projection extends along the long axis of a single optic column to which it, but not necessarily its collaterals, is restricted.
This definition follows Fischbach and Dittrich (1989) in classifying based on the primary projection. A neuron with broad and extensive collaterals with terminals in adjacent columns is still classified as a columnar neuron under this definition. Other treatments have classified such neurons as tangential.
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).
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.
A segmental subdivision of the nervous system.
A supporting cell of the nervous system.
Progenitor cell that gives rise only to glial cells and not neurons (Hartenstein, 2011).
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).
Adult neurogenesis demonstrated in the adult optic lobe in response to injury (Fernandez-Hernandez et al., 2013).
Daughter cell formed through asymmetric division of a neuroblast, typically generating two postmitotic neurons.
Multicellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system.
Any somatic cell (FBbt:00100318) that overlaps some sense organ (FBbt:00005155).
Precursor cell that gives rise to at least one cell of an external sensory organ.
First-order precursor cell: mother of all the clonally related cells of an external sensory organ.
external sensory organ sensory mother cell
Sensory organ that has external structures that detect mechanical or chemical stimuli.
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).
Nuclear divisions 1 and 2. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
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).
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).
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).
A blastoderm embryo prior to cellularization (corresponds to embryonic stages 3 and 4).
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).
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).
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).
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).
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).
Adult and larval hindguts express the transcription factor brachyenteron (Sawyer et al., 2017).
The sum of all the structures in the embryo that will develop into the embryonic/larval integumentary system.
presumptive embryonic/larval integumentary system
Integumentary system of the late embryo or larva.
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.
Anlage in statu nascendi of the visual system in a stage 5 embryo that will give rise to the visual system anlage.
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).
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).
Anlage of the visual system in the gastrula embryo that will give rise to the visual primordium.
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).
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.
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.
Ventral region of the trunk ectoderm, which gives rise to the ventral epidermis and the central nervous system (Stathopoulos and Newcomb, 2020).
Any glial cell (FBbt:00005144) that is part of some lamina anlage (FBbt:00001939).
Cuboidal glial cell found in the visual system of larvae and adults, located more distal than the row of marginal glial cells. These glial cells contact marginal glia at their base (proximal) and satellite glia at their apex (distal), and constitute the only class of cells with nuclei in the neuropil proper, in the distal lamina.
Specialized ensheathing glial cell of the lamina (Edwards et al., 2012; Kremer et al., 2017). These cells form a contiguous layer at the proximal surface of the lamina and associate with multiple lamina columns (Edwards et al., 2012; Kremer et al., 2017). Their processes extend into the lamina, ensheathing proximal parts of the cartridges (Kremer et al., 2017). They also extend protrusions proximally into the outer chiasm (Kremer et al., 2017). It is between the marginal glial cells and epithelial glial cells that the R1-R6 growth cones terminate (Poeck et al., 2001; Winberg et al., 1992). There are around 100 of these cells per lamina (Kremer et al., 2017).
Cell body glial cell of the lamina. Unlike in other cell body rind regions of the brain, the cell body glia of the lamina form two distinct layers and multiple neuronal cell bodies may be found in one glial pocket (Kremer et al., 2017).
Glial cell located in the medulla neuropil. There are at least three subtypes of reticular glia and at least two subtypes of ensheathing glia (Kremer et al., 2017).
adult medulla neuropil associated glial cell
Epidermis of the ventral region of the embryo.
Ventral halve of an embryonic apodeme. The discontinuity between dorsal and ventral halves is visible on a lateral view.
Plate or plates that surrounds the anus.
Visual organ of the larva that is anchored to the basal surface of the thin epithelium of the dorsal pouch, lateral to the musculature of the pharynx (Green et al., 1993; Hartenstein et al., 2019). It consists of a dense cluster of approximately 12 photoreceptor neurons and no support cells (Green et al., 1993; Hartenstein et al., 2019). It is connected to the brain via the Bolwig nerve (Green et al., 1993).
Location in ocular segment on basis of FBrf0075072.
Any sense organ (FBbt:00005155) that is part of some antennal segment (FBbt:00000009).
Chiasma lying between the lamina and medulla of the optic lobe (Ito et al., 2014). Axons reverse the anterior-posterior order between the lamina and the medulla, with axons from the anterior lamina cartridges projecting to the posterior medulla columns (Ito et al., 2014).
A tract of crossing fibers, that remaps or systematically permutates the linear order between two neuropils.
Primordium of the late extended germ band and closure embryo that gives rise to the larval outer optic anlage. It develops from the posterior lip of the visual primordium.
Primordium of the embryo that gives rise to the larval Bolwig organ. It develops from the most posterior region of the visual primordium, remaining attached to the surface as the rest of the optic placode becomes internalized during stages 12-13 (Green et al., 1993). It consists of approximately 12 cells, which begin to differentiate into photoreceptors during stage 13 (Green et al., 1993). During stages 15-16, the photoreceptors move out of the epidermis and come to lie attached to the outer lining of the dorsal pouch (Green et al., 1993).
Peripheral nervous system of the embryo or larva.
embryonic/larval peripheral nervous system
An eye photoreceptor cell whose rhabdomere is part of the outer trapezoid of rhabdomeres of each ommatidium. There are six of these per ommatidium. Each has a single axon that projects along a single lamina optic cartridge within which it makes extensive synaptic connections before terminating in the proximal lamina. It is strongly presynaptic to lamina monopolar neurons L1 and L2 and the lamina intrinsic (amacrine) neuron (Rivera-Alba et al., 2011).
Eye photoreceptor cell whose rhabdomere is located in the center of each ommatidium.
Photoreceptor cell that forms the core of each ommatidium in the adult eye. Eight of these photoreceptors are arranged in each ommatidial core, bundled like the staves of a barrel. Each has a photosensitive rhabdomere that projects into the barrel cavity and adjacent supporting membrane, the stalk (Wolff and Ready, 1993). Each extends an axon into the optic lobe. Activation of the photoreceptor by light results in depolarization and in histamine release at the synapses of these axons (Sarthy, 1991).
Note - eyelet photoreceptors are NOT sub-types.
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.
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.
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
Portion of tissue, that consists of one or more layers of cells with distinct apical-basal polarity, connected to each other by cell junctions.
Somatic cell that is a precursor to a mature cell.
Anatomical structure that is a primary subdivision of whole organism. The mereological sum of these is the whole organism.
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.
Undifferentiated cell which retains its identity while budding off cells which differentiate.
An epithelium consisting of columnar shaped cells.
The region of the ectoderm posterior to the cephalic furrow.
The cerebral ganglion, minus the optic lobes. It includes part of the protocerebrum (without the optic lobes), the deutocerebrum and the tritocerebrum.
Dorsolateral horn-shaped synaptic neuropil domain of the adult protocerebrum that houses the terminals of various antennal lobe projection neurons (Ito et al., 2014). It is not separated from other neuropils by a glial sheath, but by the extent of arborization and synapsing of these antennal lobe projection neurons (Ito et al., 2014).
Lateral synaptic neuropil domain of the adult superior neuropils. It lies behind the anterior optic tubercle, in front of the mushroom body calyx and above the superior clamp and lateral horn. Its boundary with the anterior optic tubercle (AOTU), mushroom body calyx and lateral horn is demarcated by the extent of arborization of visual projection neurons and antennal lobe projection neurons. Boundaries with the superior clamp, anterior and posterior ventro-lateral protocerebrum are defined using clearly distinguishable fiber bundles.
Boundaries defined by Ito et al. (2014) (used to define this term) differ slightly from those defined for slpr in Otsuna and Ito, 2006. The anterior superior SLP corresponds to mslpr and the posterior superior SLP to pslpr of Otsuna and Ito (2006). The SLP also corresponds to the lateral part of the dorsolateral protocerebrum (DLP) and lateral part of the inner dorsolateral protocerebrum (IDLP) of Chiang et al. (2011) (Ito et al., 2014).
A large mass of synaptic neuropil domains in the anterior brain of the adult, between the antennal lobe and the optic lobe (Ito et al., 2014). It can be divided into an anterior and posterior regions (AVLP and PVLP) (Ito et al., 2014).
Currently some uncertainty about whether this is truly protocerebral - may actually be part of deutocerebrum (Strausfeld has characterized it as such). This should be clarified as a result of Volker Hartenstein's lineage mapping work. The VLP corresponds to almost all of the vlpr of Otsuna and Ito (2006) and to the ventrolateral protocerebrum (VLP) and optic glomerulus (OG) of Chiang et al. (2011) (Ito et al., 2014).
Synaptic neuropil domain of the adult protocerebrum that receives extensive arborizations from visual projection neurons from the lobula and the medulla, projecting via the anterior optic tract. It protrudes from the anterior-most area of the ventro-lateral neuropils and is slightly detached from the ventro-lateral protocerebrum. This neuropil is absent from the larval brain, being formed during pupal development.
Otsuna and Ito (2006) suggest that the optic tubercle may be divided into three regions according to the density of arborizations. The medial-most (optu1) and lateral-most (optu3) contain dense arborizations of the Lcn10 neurons, whilst the area between these regions (optu2) is essentially devoid of the lobula columnar neurons.
A structure mainly consisting of cell components, rather than complete cells.
May contain some complete cells in addition to partial ones (e.g. glia in nervous system regions).
One of a group of synaptic neuropil domains of the larval brain which are located ventral to the mushroom body and are grouped around the long axon tracts connecting the larval protocerebrum to the ventral nerve cord. This medially located compartment contacts the antennal lobe posteriorly. The lateral cervical tract ascends through the center of this compartment. It is the larval counterpart of the adult ventromedial neuropils.
Note - description of relative location of brain structures in this definition is based on Younossi-Hartenstein et al., 2003 description of the first instar larval brain and Pereanu et al., 2010 third instar larval brain.
Thin layer of larval synaptic neuropil found lateral to the superior medial protocerebrum, separated from it by axon bundles of the DPlc lineages (Hartenstein et al., 2015). It is the precursor to the adult superior lateral protocerebrum and lateral horn domains (Pereanu et al., 2010; Hartenstein et al., 2015).
dorsal centro-posterior lateral synaptic neuropil domain
embryonic/larval superior lateral protocerebrum
One of a group of synaptic neuropil domains of the larval brain which are located ventral to the mushroom body and are grouped around the long axon tracts connecting the larval protocerebrum to the ventral nerve cord. This compartment contacts the antennal lobe posteriorly, and is lateral to the lateral accessory lobe and ventromedial cerebrum. It grows anteriorly during larval development. It is the larval counterpart of the adult ventrolateral protocerebrum.
baso-posterior lateral synaptic neuropil compartment
baso-posterior lateral synaptic neuropil domain
Developmental relation to adult synaptic neuropil domains comes from a personal communication from Volker Hartenstein. Note - description of relative location of brain structures in this definition is based on Younossi-Hartenstein et al., 2003 description of the first instar larval brain and Pereanu et al., 2010 third instar larval brain.
embryonic/larval ventrolateral protocerebrum
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.
cell body rind of the central nervous system
The sum of all the developing presumptive components of a specific embryonic/larval system in an embryo.
Glial layer that largely surrounds a region of synaptic neuropil in the central nervous system (Younossi-Hartenstein et al., 2003). It is mainly formed by synaptic neuropil ensheathing glia, but these cells also frequently branch into neuropil domains and the layer also contains nuclei of reticular glia (Kremer et al., 2017).
Larval counterpart to the adult periesophageal neuropils (Pereanu et al., 2010). It is located adjacent to the esophagus and guides the medial cervical tract (Younossi-Hartenstein et al., 2003; Hartenstein et al., 2015). Its anterior portion corresponds to the tritocerebrum (Hartenstein et al., 2015).
embryonic/larval periesophageal neuropils
Portion of the eye disc which is posterior to the morphogenetic furrow. It contains developing ommatidial clusters whose maturity increases with distance posterior to the furrow.
eye disc posterior to the morphogenetic furrow
Deutocerebrum of the adult brain. Substantial portions are below the level of the esophagus (Ito et al., 2014).
Tritocerebrum of the adult brain. Substantial portions are below the level of the esophagus (Ito et al., 2014).
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.
Any neuron (FBbt:00005106) that is capable of some acetylcholine secretion, neurotransmission (GO:0014055).
Any neuron (FBbt:00005106) that is capable of some gamma-aminobutyric acid secretion, neurotransmission (GO:0061534).
Some GABAergic neurons express ChAT transcripts (and reporters) at low levels, but do not produce functional enzyme (Lacin et al., 2019 - FBrf0242251).
A cluster of cells of various types which form a discrete structure with a largely bona fide boundary.
An anatomical structure consisting of multiple cell cluster organs and which does not contain portions of tissue.
Sensillum which is embedded in the body wall and has a specific cuticular structure involved in the transduction of some sensory signal as a part.
This is a parent term for the mechanosensory bristles referred to as external sensilla (es) in some references e.g. Tsubouchi et al., 2017 (FBrf0237124), but also includes other modalities.
Sensillum that is internal to the animal - i.e. having no part that is part of the cuticle.
Any compound cell cluster organ (FBbt:00007230) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
Compound sense organ that is located within the epidermis.
Any sensillum (FBbt:00007152) that is part of some adult head (FBbt:00003007).
Any sensillum (FBbt:00007152) that is part of some larval head (FBbt:00001730).
Specialized structure that is found on the cuticle.
Photoreceptor cell that contains rhabdomeres.
Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all continuous with each other.
Anatomical group whose component anatomical structures lie in close proximity to each other.
An anatomical group whose component structures share a common function.
Any sense organ (FBbt:00005155) that is part of some larval head (FBbt:00001730).
Specialized structure that is found on the integument.
Any nerve (FBbt:00005105) that is part of some larval head (FBbt:00001730).
The part of some organism that is part of some specified segment.
Any larval sense organ (FBbt:00002639) that is part of some intercalary segment (FBbt:00000010).
embryonic/larval intercalary segment sense organ
Stem cell that is a progenitor of somatic cells.
Any neuron (FBbt:00005106) that is capable of some histamine secretion, neurotransmission (GO:0061538).
A neuron that uses a biogenic amine as its neurotransmitter (Vomel and Wegener, 2008; Fuchs et al., 2014).
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.
Sense organ that is internal to the animal - i.e. having no part that is part of the cuticle.
An interneuron that projects from some primary sensory neuropil (e.g. the antennal lobe) to a higher neuropil region.
A neuroblast that is located in the larval outer optic anlage and that will give rise the to neurons of the adult lamina and outer medulla. It develops from a neuroepithelial cell in the medial region of the outer optic anlage. Neuroblasts in the medial edge give rise to the outer medulla neurons, whereas neuroblasts at the lateral edge give rise to lamina neurons.
A tract of the central nervous system that does not cross the midline.
Structure consisting of the embryonic/larval foregut, midgut and hindgut.
Structure consisting of a simple epithelium surrounded by visceral muscles, nerves and tracheae. The adult gut is divided into the adult foregut, midgut and hindgut regions, based on developmental origin.
Any neuron (FBbt:00005106) that synapses restricted to region some adult optic lobe (FBbt:00003701).
A columnar neuron whose arborizations are restricted to the adult optic lobe.
Interneuron that is oriented perpendicular to the columns of adult optic lobe neuropils and has a major projection along the plane of a layer of optic lobe neuropil.
A group of trichomes covering a region of integument.
A subdivision of the optic lobe neuropil that maps to a single ommatidium. In the lamina and distal medulla these correspond to the projections and arborization of photoreceptor cells. Narrow field columnar neurons define continuation of these columns medial to this.
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.
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception.
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.
Any neuron (FBbt:00005106) that capable of part of some sensory perception (GO:0007600).
Glutamatergic (Gao et al., 2008; Karuppudurai et al., 2014) distal medullary amacrine neuron that branches extensively in medulla layer M6A (Fischbach and Dittrich, 1989; Takemura et al., 2013; Nern et al., 2015), spanning approximately 16 medulla columns (Karuppudurai et al., 2014), with centrifugal projections back to layer M4 (Takemura et al., 2013; Nern et al., 2015). The highest arbor density and longest distal projection are usually found in one optic column (its 'home column'), near the center of the M6A arborization, with these columns tiling between different individual Dm8 cells, while the rest of the arbor overlaps with other Dm8 cells considerably (Gao et al., 2008; Nern et al., 2015; Kind et al., 2021). In layer M6, it is postsynaptic to several R7 photoreceptor cells and presynaptic to Tm5c (Gao et al., 2008; Takemura et al., 2013; Karuppudurai et al., 2014). The contacts with Tm5c are clustered in one column at the center of the dendritic field of Dm8 (Karuppudurai et al., 2014). It is involved in UV preference (Gao et al., 2008).
Connectivity inferred from EM reconstructions from a single EM section. The neurotransmitter was assessed in cells labelled with a glutamate GAL4 driver P\{GawB}vGlut[OK371] (FBti0076967) (Gao et al., 2008), RT-PCR and by immunohistochemistry (Karuppudurai et al., 2014). Connectivity with R7 was assessed by EM reconstruction of a single medulla column (Gao et al., 2008) or reconstruction of serial-section TEM (Takemura et al., 2013).
A transmedullary neuron that arborizes across multiple columns.
A transmedullary neuron whose arborizations are mostly restricted to a single column.
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.
Primordium of the anal pad of the late extended germ band and dorsal closure embryo that will give rise to the embryonic anal pads.
Anlage of the ventral apodeme of the late extended germ band embryo that will give rise to the ventral apodeme primordium.
Primordium of the ventral apodeme of the dorsal closure embryo that will give rise to the ventral apodemes.
Primordium of the denticle field of the dorsal closure embryo that will give rise to the larval denticle fields.
Region of embryonic and larval ventral cuticle that displays denticle belts. It develops from the denticle field primordium.
Any anatomical entity (FBbt:10000000) that develops from some ectoderm (FBbt:00000111).
Any anatomical entity (FBbt:10000000) that develops from some anterior ectoderm (FBbt:00000119).
Any anatomical entity (FBbt:10000000) that develops from some ventral ectoderm (FBbt:00005558).
A group of synaptic neuropil domains in the adult brain located above or and lateral to the esophagus, below the mushroom body calyx and inferior neuropils, behind the lateral accessory lobe and medial to the ventrolateral neuropils.
Despite the name, intended as a singular noun as in "The United States".
The sum of all the anlagen and primordia that will develop into a single system.
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.
The part of the neuropil consisting largely of neuron projections without synapses.
The part of the neuropil consisting largely of synapsing neuron projections.
Synaptic neuropil region that is a subdivision of a synaptic neuropil domain.
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.
Laminar or concentric subdivision of a synaptic neuropil domain along its long axis delimited by a discontinuity in synaptic or fiber density.
Layer of the lobula that is fifth-most from the second optic-chiasm. It extends from the terminal arborizations of translobula plate neuron Tlp1 at the border of the fourth layer, to the extensive arborizations of lobula tangential neuron LT7, which defines layer 6.
A glomerular, bilaterally paired synaptic neuropil domain lying in front of the posterior lateral protocerebrum (PLP), and above the wedge. The great commissure is at the boundary in the mid-level between the PLVP and PLP. It is contiguous with posterior lateral protocerebrum (PLP), which lies behind it. It houses many optic glomeruli formed by the terminals of neurons projecting from the optic lobe, primarily from the lobula. The boundary with the PLP, except at mid-level, is defined as the boundary between these glomeruli with different origins (lobula or lobula plate).
A bilaterally paired synaptic neuropil domain of the adult that contains many glomeruli and is located behind the posterior ventrolateral protocerebrum (PVLP) and above the wedge. The mid-level of the posterior lateral protocerebrum (PLP) is separated from the PVLP by the great commissure, but above and below this the two neuropils are contiguous. The PLP houses many optic glomeruli formed by the terminals of neurons projecting from the optic lobe, primarily from the lobula plate. The boundary with the PVLP is defined by the boundary between these glomeruli that have different origins (lobula or lobula plate).
The PLP corresponds to almost all of the plpr of Otsuna and Ito (2006) and to the caudal ventrolateral protocerebrum (CVLP) and lateral part of the superpeduncular protocerebrum (SPP) of Chiang et al. (2011) (Ito et al., 2014).
Laminar or radial subdivision of a synaptic neuropil domain along its short axis delimited by a discontinuity in synaptic or fiber density.
Synaptic neuropil domain of the adult brain that is the inferior (ventral) part of the posterior cerebral ganglion, covering the area between the inferior bridge and the gnathal ganglion with its superior part lying behind the ventral complex. It contains extensive arborizations of ascending and descending neurons. Its superior boundary is the level above which such arborizations do not occur. It also contains the terminals of axons from the ocellar ganglia, projecting via the ocellar nerves.
The ventral complex corresponds to the caudal medial protocerebrum (CMP) and possibly includes part of the ventromedial protocerebrum (VMP) of Chiang et al. (2011) (Ito et al., 2014).
A closely associated group of synaptic neuropil domains.
Region of the medulla excluding the medulla dorsal rim area.
A synaptic neuropil block in the adult brain consisting of the two medial-most synaptic neuropil domains of the optic lobe: the lobula and the lobula plate.
Synaptic neuropil block in the adult brain located along the ventrolateral side of the adult central brain.
An aglomerular, bilaterally paired synaptic neuropil domain that is the inferior-most domain of the ventrolateral neuropils, lying between the anterior and posterior ventrolateral protocerebrum (AVLP and PVLP) and posteriorlateral protocerebrum (PLP), and the saddle and gnathal ganglion. The wedge is lateral to the inferior fiber system and vest. It receives synaptic input from the saddle and the antennal mechanosensory and motor center (AMMC) within it. This includes direct sensory input from antennal mechanosensory neurons that also innervate the AMMC.
The anterior wedge corresponds to the inferior part of the vlpr of Otsuna and Ito (2006); the posterior wedge corresponds to part of the plpr (Ito et al., 2014).
A block of synaptic neuropil domains in the adult brain arranged in a layer covering the superior (dorsal) surface of the brain. In encompasses the superior intermediate, superior lateral and superior medial protocerebrum.
Despite the name, intended as a singular noun as in 'The United States'.
Inferior (ventral) part of the posterior slope. It flanks both sides of the esophagus, and is posterior and medial to the wedge. Below the plane of the inferior VLP commissure and the posterior optic commissure.
The IPS corresponds to part of the psl of Otsuna and Ito (2006) and to the ventral postcommissural ventromedial cerebrum (Ito et al., 2014).
Group of synaptic neuropil domains in the adult brain located between the antennal lobe/ventromedial neuropils and above the gnathal ganglia. In addition, it includes one synaptic domain that is part of the ventral cerebral ganglion-the prow.
Despite the name, it is intended as a singular noun as in "The United States".
Synaptic neuropil domain covering the dorsal and posterior surface of the adult gnathal ganglia. It contains the antennal mechanosensory and motor center (AMMC).
The saddle corresponds to the antennal mechanosensory and motor center (AMMC) of Chiang et al. (2011) and to the lateral and ventromedial periesophageal neuropils (Ito et al., 2014).
A neuron that is part of the adult nervous system. These can be born during the postembryonic phase of neurogenesis (Lacin and Truman, 2016) or they can develop from larval neurons during the pupal stage (Veverytsa and Allan, 2013).
Neuron that is born during the second round of neurogenesis, which commences during the larval stage, after a period of neuroblast quiescence (Lacin and Truman, 2016).
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.
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.
Larval neuron that does not extend neurites beyond the optic neuropil.
Larval neuron that relays signals from the optic neuropil to higher brain areas. Many of these receive input from Rh5 photoreceptor cells.
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of light.
Any neuron (FBbt:00005106) that capable of part of some sensory perception of light stimulus (GO:0050953).
Polarized glial cell with a flattened cell body that forms a sheath around the synaptic and tract neuropil regions (Hartenstein, 2011; Pogodalla et al., 2021). They may serve a homologous function to the wrapping glia, which ensheath the peripheral nerves (Kremer et al., 2017).
ensheathing neuropil associated glial cell
Ensheathing glial cell of the larva. There are approximately 112 of these cells in the third instar central nervous system (Pogodalla et al., 2021). Some of these cells are polyploid, but others can undergo cell division during the pupal stage to generate adult glia (Kato et al., 2020).
embryonic/larval ensheathing neuropil associated glial cell
Astrocyte-like glial cell of the embryonic/larval central nervous system. There are approximately 15 of these cells in each brain hemisphere (Omoto et al., 2015) and 6 per ventral nerve cord hemineuromere (Peco et al., 2016) throughout larval development. They appear to endoreplicate and increase in size, then die during metamorphosis (Omoto et al., 2015; Kato et al., 2020).
embryonic/larval astrocyte-like neuropil associated glial cell
embryonic/larval dendritic neuropil associated glial cell
embryonic/larval reticular neuropil associated glial cell
embryonic/larval reticular neuropil-associated glial cell
embryonic/larval astrocyte-like glial cell
Neuropil associated glial cell of the adult central nervous system that has a dendritic morphology and elaborates inside the associated synaptic neuropil (Awasaki et al., 2008). Their nuclei are found at synaptic neuropil surfaces and they extend branched filiform or lamelliform processes that pervade the neuropil (Hartenstein, 2011).
adult astrocyte-like neuropil associated glial cell
adult dendritic neuropil associated glial cell
adult reticular neuropil associated glial cell
adult reticular neuropil-associated glial cell
Any neuropil glial cell (FBbt:00001303) that is part of some larval brain (FBbt:00001920).
Glial cell that is part of the glial sheath surrounding the neuropil of the adult brain.
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).
Precursor of neuropil associated glia of the adult central brain. It arises from a type II neuroblast in the central brain during larval development. Different neuroblasts generally contribute to glia of different adult brain regions. These precursors clonally expand during metamorphosis, spread out across the neuropil surfaces and mature into adult glia.
Some of these cells migrate to the optic lobe, but optic lobe-born glia do not migrate to the central brain (Omoto et al., 2015).
precursor of adult central brain neuropil glia
Astrocyte-like glial cell of the adult central brain. These cells have their nuclei at synaptic neuropil surfaces throughout the central brain (not just adjacent to the cell body rind) and they extend processes into the synaptic and/or tract neuropil (Kremer et al., 2017). They have variable size and morphology and one cell may project into more than one neuropil region, but cells tend to cover non-overlapping areas (Kremer et al., 2017). Reticular glial cell processes in the synaptic neuropil of the central brain tend to be more dense in neuropil regions where synaptic terminals of neurons are less dense (Kremer et al., 2017).
adult central brain reticular glial cell
adult central brain astrocyte-like glial cell
Any ensheathing glial cell (FBbt:00047836) that is part of some adult central brain (FBbt:00047887).
adult central brain ensheathing glial cell
Adult brain excluding the optic lobes. This consists of the cerebrum and the gnathal ganglion.
Neuroblast that divides symmetrically to increase neuroblast numbers before generating neurons. They arise from a spatiotemporal conversion of classical self-renewing stem cells (type I neuroblasts).
Immature neuron of the eye disc that will develop into one of the photoreceptors (R1-R8) of the adult eye.
Immature neuron of the eye disc that will develop into a photoreceptor cell R1 of the adult eye. It forms during the second mitotic wave and joins the precursor cells of the five-cell ommatidial precursor cluster to form the eight-cell ommatidial precursor cluster.
Immature neuron of the eye disc that will develop into a photoreceptor cell R2 of the adult eye. It forms during the first mitotic wave and is part of the ommatidial precursor cluster from the early stage.
Immature neuron of the eye disc that will develop into a photoreceptor cell R3 of the adult eye. It forms during the first mitotic wave and is part of the ommatidial precursor cluster from the early stage.
Immature neuron of the eye disc that will develop into a photoreceptor cell R4 of the adult eye. It forms during the first mitotic wave and is part of the ommatidial precursor cluster from the early stage.
Immature neuron of the eye disc that will develop into a photoreceptor cell R5 of the adult eye. It forms during the first mitotic wave and is part of the ommatidial precursor cluster from the early stage.
Immature neuron of the eye disc that will develop into a photoreceptor cell R6 of the adult eye. It forms during the second mitotic wave and joins the precursor cells of the five-cell ommatidial precursor cluster to form the eight-cell ommatidial precursor cluster.
Immature neuron of the eye disc that will develop into a photoreceptor cell R7 of the adult eye. It forms during the second mitotic wave and joins the precursor cells of the five-cell ommatidial precursor cluster to form the eight-cell ommatidial precursor cluster.
Immature neuron of the eye disc that will develop into a photoreceptor cell R8 of the adult eye. It forms during the first mitotic wave and is part of the ommatidial precursor cluster from the early stage.
Neuron that projects from the adult optic lobe to the central brain, conveying information from light stimuli.
Neuron that projects from the optic lobe to the central brain, conveying information from light stimuli.
Small neuropil compartment of the larval optic lobe that contains the axons of photoreceptors. It is the first center for visual processing in the larval brain. It is largely surrounded by the outer optic anlage at earlier developmental stages and becomes sandwiched between the developing proximal medulla and the inner optic anlage by third instar. It is incorporated into the adult optic lobe as the accessory medulla.
Adult neuron that has dendritic arbors in the lateral horn (including local neurons). Many of these receive olfactory input from antennal lobe projection neurons.
In contrast to previous usage, Dolan et al. (2019) (FBrf0242477) use 'lateral horn neuron' to refer to any neuron associated with the lateral horn, including input neurons. This class only includes neurons with dendritic arborizations in the lateral horn.
Any synaptic neuropil layer (FBbt:00040008) that is part of some medulla (FBbt:00003748).
Any synaptic neuropil layer (FBbt:00040008) that is part of some lobula (FBbt:00003852).
Any synaptic neuropil layer (FBbt:00040008) that is part of some lobula plate (FBbt:00003885).
Any projection neuron (FBbt:00007392) that receives synaptic input in region some wedge (FBbt:00045027).
Adult neuron with its arbors mostly restricted to the lateral horn.
Glial cell of the adult that is associated with the cell body rind of the central brain. One cell can wrap around 20 to 100 cell bodies, but some cell bodies are wrapped by two neighboring glial cells (Kremer et al., 2017). They have an overall globular shape with fine lamellae protruding into surrounding areas (Kremer et al., 2017).
adult central brain cortex associated glial cell
adult central brain cell body glial cell
Astrocyte-like (reticular) glial cell located in the adult medulla neuropil. There are at least three subtypes and they show tiling and have a high structural density (Kremer et al., 2017).
Ensheathing glial cell located in the adult medulla neuropil. There are at least two subtypes, forming a dense sheath around the distal medulla and serpentine layer, where their cell bodies are found (Kremer et al., 2017). Rather than having its own ensheathing glia, the proximal medulla is invaded by fine processes from the inner chiasm glia (Kremer et al., 2017).
Glial cell located in the cell body rind of the medulla. It is similar to cell body glial cells of the central brain (Kremer et al., 2017).
Astrocyte-like (reticular) glial cell with its soma at the surface of either the adult lobula or lobula plate (lobula complex) neuropil regions (Kremer et al., 2017). These cells take many shapes and sizes and may form branches into one or both neuropils (Kremer et al., 2017).
adult lobula complex reticular glial cell
Cells additionally projecting into the medulla are mentioned, but not shown in images or diagram, by Kremer et al. (2017). Not clear if these should fall under this class - part_of may need revising - https://orcid.org/0000-0002-1373-1705.
adult lobula complex astrocyte-like glial cell
Ensheathing glial cell with its soma at the surface of the either the lobula or lobula plate (lobula complex) neuropil regions (Kremer et al., 2017). These cells form columnar processes perpendicular to the neuropil margin, as well as tangential processes parallel to the margin (Kremer et al., 2017). They form a complex three-dimensional arrangement of branches (Kremer et al., 2017).
adult lobula complex ensheathing glial cell
Any neuron (FBbt:00005106) that synapses restricted to region some embryonic/larval lateral horn (FBbt:00111688).
Neuron belonging to a hemilineage that has active Notch signaling.
Neuron belonging to a hemilineage that does not have active Notch signaling.
Secondary neuron belonging to a hemilineage that has active Notch signaling.
Secondary neuron belonging to a hemilineage that does not have active Notch signaling.
Superficial layer of neuronal cell bodies and glia that overlies the neuropil of the larval central nervous system.
cell body rind of larval central nervous system
Superficial layer of neuronal cell bodies and glia that overlies the neuropil of the adult central nervous system (brain or ventral nerve cord).
cell body rind of adult central nervous system
Glial cell located amongst neuronal cell bodies in the cortex of the embryonic/larval brain.
embryonic/larval brain cortex glial cell
Astrocyte-like (reticular) glial cell found in the optic lobe (Kremer et al., 2017).
adult optic lobe astrocyte-like glial cell
Adult neuron that ascends from the subesophageal zone (Otto et al., 2020).
Potential gustatory projection neurons (Otto et al., 2020).
Adult cell body rind region that overlies the posterior surface of the lobula plate (Ito et al., 2014).
cell body rind of adult posterior lobula plate
Neuropil mass below the larval esophagus consisting of the gnathal ganglion and part of the tritocerebrum.
This is analogous to the adult term based on Ito et al. (2014), reflecting location relative to the esophagus, rather than segmental identity.
Neuropil mass below the esophagus encompassing the three gnathal neuromeres and any regions of the cephalic (supraesophageal) neuromeres situated below the esophagus (Ito et al., 2014).
Neuropil mass above the esophagus (Ito et al., 2014). It is part of the cerebral (supraesophageal) ganglion (Ito et al., 2014).
Neuropil mass above the larval esophagus consisting of the protocerebral and deutocerebral neuromeres and part of the tritocerebrum.
Any neuron (FBbt:00005106) that has synaptic IO in region some embryonic/larval lateral horn (FBbt:00111688).
Region of the adult anterior optic tubercle that receives input from neurons that project from the medulla (Timaeus et al., 2020). It consists of the anterior optic tubercle excluding the medial zone (large unit) (Timaeus et al., 2020). It can be further subdivided based on the innervation patterns of medulla-tubercle and tubercle-bulb neurons (Timaeus et al., 2020).
Neuron that connects the medulla to the anterior optic tubercle (AOTU), via the anterior optic tract, innervating the small unit of the AOTU (Timaeus et al., 2020; Hulse et al., 2021; Kandimalla et al., 2023). It is derived from an optic neuroblast (Kandimalla et al., 2023). There are around 500 of these cells per hemisphere (Nern et al., 2025).
Descending neuron of the larva with its soma in the brain and processes extending into the subesophageal zone (Winding et al. (2023).
Winding et al. (2023) appear to exclude neurons that continue to the VNC, but these are not excluded from this class.
Descending neuron of the larva with its soma in the brain and processes extending further into the CNS, reaching the gnathal ganglion or ventral nerve cord (Winding et al. (2023).
Ignores directionality of information flow, similar to 'adult descending neuron'.
Synaptic neuropil subdomain of the adult subesophageal zone that houses the axon terminals of sensory neurons (Miyazaki and Ito, 2010; Kendroud et al., 2018). Larger domains can be defined based on the projection patterns of neurons entering the brain via particular roots of the maxillary-labial, pharyngeal and antennal nerves (Kendroud et al., 2018). Many smaller domains, usually subdomains of the larger regions, can also be defined based on neuron morphology and function (Miyazaki and Ito, 2010; Munch et al., 2022).
adult labellar gustatory association center
adult pharyngeal gustatory association center
adult sensory region of subesophageal zone
Neuropil region of the larval central nervous system that is defined by the axonal projections of sensory neurons (Kendroud et al., 2018; Miroschnikow et al., 2018).
Neuron that is in a transient state between birth and its first mature morphology or between its larval and adult morphologies.
Neuron that is in a transient, immature, state between birth and its first mature morphology.
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.
Neuron that transmits information out of the central nervous system (CNS). It has its soma in the cell body rind of the CNS, a dendrite in the CNS and an axon projecting through a nerve (Prokop, 2006).
Region of the larval cell body rind that overlies the neuropil of the larval tritocerebrum.
Region of the adult brain cell body rind that overlies the protocerebrum.
Region of the adult brain cell body rind that overlies the neuropil of the tritocerebrum.
Region of the larval cell body rind that overlies the neuropil of the larval deutocerebrum.
Region of the larval cell body rind that overlies the neuropil of the larval protocerebrum.
Optic column that maps to a single yellow ommatidium.
Optic column that maps to a single pale ommatidium.
Visual projection neuron that has tangential arborization in the medulla (Kind et al., 2021).
medullary tangential visual projection neuron
medulla tangential visual projection neuron
Intrinsic neuron of the medulla that has a tangential arborization pattern (Kind et al., 2021).
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).
Many recent papers do not count the pharyngeal and labral taste neurons as 'enteric neurons', hence only a narrow synonym.
Any gut-innervating neuron of the adult.
Any gut-innervating neuron of the larva.
Dorsalmost layer of larval synaptic neuropil domains, found dorsal to the inferior protocerebrum (Hartenstein et al., 2015).
Immature secondary neuron that is a precursor to an adult T4 neuron (Hormann et al., 2020). It is generated from a neuroblast that amplifies by symmetric division (type III) before generating the T4 (and T5) neurons (Mora et al., 2018). During its development, it first projects its axon to the appropriate lobula plate layer, then forms its dendrites in medulla layer 10 (Hormann et al., 2020).
Immature secondary neuron that is a precursor to an adult T5 neuron (Hormann et al., 2020). It is generated from a neuroblast that amplifies by symmetric division (type III) before generating the T5 (and T4) neurons (Mora et al., 2018). During its development, it first projects its axon to the appropriate lobula plate layer, then forms its dendrites in lobula layer 1 (Hormann et al., 2020).
Immature form of the distal medullary amacrine neuron Dm8a (Konstantinides et al., 2022). It is a Notch OFF hemilineage secondary neuron, born from a medulla forming neuroblast during the Hbn/Opa/Slp temporal window (Konstantinides et al., 2022).
immature distal medullary amacrine neuron Dm8
immature distal medullary amacrine neuron Dm8a
Immature form of the lamina intrinsic neuron (Konstantinides et al., 2022). It is a Notch OFF hemilineage secondary neuron, born from a medulla forming neuroblast during the Hbn/Opa/Slp temporal window (Konstantinides et al., 2022).
Immature form of the medullary intrinsic neuron Mi1 (Konstantinides et al., 2022). It is a Notch ON hemilineage secondary neuron, born from a medulla forming neuroblast during the Hth temporal window (Konstantinides et al., 2022).
Immature form of the medullary intrinsic neuron Mi4 (Konstantinides et al., 2022). It is a Notch OFF hemilineage secondary neuron, born from a medulla forming neuroblast during the Hth/Opa temporal window (Konstantinides et al., 2022).
Immature form of the medullary intrinsic neuron Mi9 (Konstantinides et al., 2022). It is a Notch OFF hemilineage secondary neuron, born from a medulla forming neuroblast during the Opa/Erm temporal window (Konstantinides et al., 2022).
Immature form of the columnar neuron T1 (Konstantinides et al., 2022). It is a Notch OFF hemilineage secondary neuron, born from a medulla forming neuroblast during the D/BarHI temporal window (Konstantinides et al., 2022).
Immature form of the transmedullary neuron Tm1 (Konstantinides et al., 2022). It is a Notch ON hemilineage secondary neuron, born from a medulla forming neuroblast during the Hth/Opa temporal window (Konstantinides et al., 2022).
Immature form of the transmedullary neuron Tm2 (Konstantinides et al., 2022). It is a Notch ON hemilineage secondary neuron, born from a medulla forming neuroblast during the Hth/Opa temporal window (Konstantinides et al., 2022).
Immature form of the transmedullary neuron Tm20 (Konstantinides et al., 2022). It is a Notch ON hemilineage secondary neuron, born from a medulla forming neuroblast during the Hbn/Opa/Slp temporal window (Konstantinides et al., 2022).
Immature form of the transmedullary neuron Tm3 (Tm3a) (Konstantinides et al., 2022). It is a Notch ON hemilineage secondary neuron, born from a medulla forming neuroblast during the Erm/Ey temporal window (Konstantinides et al., 2022).
Immature form of the transmedullary neuron Tm4 (Konstantinides et al., 2022). It is a Notch ON hemilineage secondary neuron, born from a medulla forming neuroblast during the Hth/Opa temporal window (Konstantinides et al., 2022).
Immature form of the transmedullary neuron Tm5b (Konstantinides et al., 2022). It is a Notch ON hemilineage secondary neuron, born from a medulla forming neuroblast during the Hbn/Opa/Slp temporal window (Konstantinides et al., 2022).
Immature form of the transmedullary neuron Tm5c (Konstantinides et al., 2022). It is a Notch OFF hemilineage secondary neuron, born from a medulla forming neuroblast during the Opa/Erm temporal window (Konstantinides et al., 2022).
Immature form of the transmedullary neuron Tm9 (Konstantinides et al., 2022). It is a Notch ON hemilineage secondary neuron, born from a medulla forming neuroblast during the Erm/Ey temporal window (Konstantinides et al., 2022).
Neuroblast that generates neurons of the optic lobe. It arises from the optic lobe neuroepithelium, with some delaminating during the embryonic stage and others delaminating during the larval stage (Hakes et al., 2018).
Ensheathing glial cell of the larval brain. There are approximately 12 of these cells in each brain hemisphere throughout larval development (Omoto et al., 2015).
embryonic/larval brain ensheathing neuropil associated glial cell
Neuropil glial cell of the adult that is derived from a larval glial cell (Kato et al., 2020). The larval astrocyte-like glia die during the pupal phase, while some of the ensheathing glia persist and divide to generate these cells (Kato et al., 2020). In the brain, these cells tend to occupy an anterior-inferior area (Kato et al., 2020).
adult primary neuropil associated glial cell
Precursor cell that can give rise to one or more sensory neurons and/or support cells of the periphery.
Secondary neuron, born after the embryonic stage, that is still in an immature state, between birth and its first mature morphology.
Immature form of a distal medullary amacrine neuron (Konstantinides et al., 2022).
immature distal medullary amacrine neuron
Immature form of a lobula columnar neuron (Konstantinides et al., 2022).
Immature form of a transmedullary neuron (Konstantinides et al., 2022).
Immature form of a centrifugal columnar neuron (Konstantinides et al., 2022).
immature optic lobe centrifugal columnar neuron
Immature neuron that will develop into an adult lamina monopolar neuron.
Immature neuron that will develop into an adult lamina monopolar neuron L1.
Immature neuron that will develop into an adult lamina monopolar neuron L2.
Immature neuron that will develop into an adult lamina monopolar neuron L3.
Immature neuron that will develop into an adult lamina monopolar neuron L4.
Immature neuron that will develop into an adult lamina monopolar neuron L5.
Region of the adult brain that receives photoreceptor input, i.e. the optic lobe or ocellar ganglion.
Any neuron with its arborizations exclusively within the medulla (Raghu and Borst, 2011).
Any neuron (FBbt:00005106) that synapses restricted to region some adult subesophageal zone (FBbt:00110639).
adult subesophageal zone intrinsic neuron
An interneuron that has distinct dendritic and axonal branches that arborize in different neuropil regions. These neurons relay information between different parts of the central nervous system.
Includes neurons with axonal and dendritic arbors in the same region if there is another branch that extends elsewhere (Frechter et al., 2019). Excludes neurons that only have a 'local' innervation pattern, where both inputs/outputs may be present on arbors that span neuropil boundaries.
Immature neuron that develops from an optic neuroblast and will become an adult optic lobe neuron.
Immature neuron that will have its synapses restricted to the optic lobe in the adult.
immature adult optic lobe intrinsic neuron
Division of an organism along its anterior-posterior axis.
anterior-posterior subdivision of organism
Any glial cell (FBbt:00005144) that is part of some cell body rind of adult optic lobe (FBbt:00111152).
Any ensheathing glial cell (FBbt:00047836) that is part of some adult optic lobe (FBbt:00003701).
Any neuropil glial cell (FBbt:00001303) that is part of some adult optic lobe (FBbt:00003701).
adult optic lobe neuropil associated glial cell
Any adult neuron (FBbt:00047095) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
Any larval neuron (FBbt:00001446) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
Glial cell located in the lamina neuropil (Kremer et al., 2017).
adult lamina neuropil associated glial cell
Neuron with its synapses restricted to the central brain.
Neuron with its synapses restricted to the primary visual centers of the adult, i.e. the optic lobes or ocellar ganglia.
Glial cell of the adult that is associated with the cell body rind of the brain or the ventral nerve cord.
Any neuron that has its soma in the central nervous system.
Any neuron that has its soma in the peripheral nervous system.
Any neuron that has its soma in the late embryonic or larval central nervous system.
embryonic/larval central nervous system neuron
Any neuron that has its soma in the adult central nervous system.
Any neuron that has its soma in the late embryonic or larval peripheral nervous system.
embryonic/larval peripheral nervous system neuron
Any neuron that has its soma in the adult peripheral nervous system.
A ganglion mother cell that is born of a type I neuroblast (Marques et al., 2023).
A ganglion mother cell that is born indirectly from a type II neuroblast. It is distinguished from type I ganglion mother cell by the expression of Sp1 (Marques et al., 2023).
Immature secondary neuron that is a precursor to an adult T neuron (Hormann et al., 2020).
Any glial cell that is found in an eye-antennal disc (Gonzalez-Blas et al., 2020).
A(n) somatic cell that is part of a(n) ectoderm anlage.
A(n) somatic cell that is part of a(n) ectoderm.
A(n) somatic cell that is part of a(n) stage 5 embryo.
An intrinsic columnar neuron of the visual system whose cell body is located in the medulla cortex and that has a main projection making wide-field arborizations in the lamina. It expresses the transcription factor Fer2 (Ozel et al., 2021) and is cholinergic (Davis et al., 2020).
A(n) somatic cell that is part of a(n) trunk ectoderm.
A(n) somatic cell that is part of a(n) anterior ectoderm.
A subdivision of the cell body rind of the central nervous system. It includes the neuronal cell bodies.
Region of the adult brain cell body rind found in the area between the central brain and the optic lobe (Ito et al., 2014). It includes the regions lateral to the anterior optic tubercle, superior lateral protocerebrum (pars lateralis), lateral horn, ventrolateral protocerebrum, wedge, saddle, inferior posterior slope and posterior lateral protocerebrum (Ito et al., 2014).
Region of the adult brain cell body rind that overlies the medulla.
Region of the adult brain cell body rind that overlies the lamina.
Region of the adult brain cell body rind that overlies the lobula.
Any neuron (FBbt:00005106) that is capable of some glutamate secretion, neurotransmission (GO:0061535).
Some glutamatergic neurons express ChAT transcripts (and reporters) at low levels, but do not produce functional enzyme (Lacin et al., 2019 - FBrf0242251).
Anatomical structure that has multiple cells as parts.
A subdivision of the gut along its long axis.
Any cell that is not a germ cell (Okada, 1998). During development, somatic cells differentiate into various types, but they do not persist beyond the lifespan of a single organism (Okada, 1998).
The entire adult 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.
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.
Tract that emerges from the medial part of the lobula (Ito et al., 2014). One branch ends in the anterior optic tubercle (AOTU) whilst the other makes a medial turn to terminate in the superior medial posterior ventrolateral protocerebrum (PVLP) of the adult brain (Ito et al., 2014). It demarcates the boundaries of the PVLP (lateral region), anterior VLP (superior and lateral region), AOTU (inferior-lateral region) and lateral horn (inferior region) (Ito et al., 2014).
Fischbach and Lyly-Hunerberg, (1983), subdivide the anterior optic tract (AOT) into four sub-bundles: S1-S4. S1 consists of 100-110 think axons surrounded by ~60 large diameter neurons that form the S2 bundle. These bundles together occupy the proximal part of the AOT close to the neuropil of the lateral protocerebrum. S3 forms the lateral ventral part of the AOT and is formed by ~430 axons of small diameter that project into the anterior optic foci. S4 is composed of approximately 660 relatively small fibers.
The main part of the lamina that does not contain the terminals of photoreceptors from dorsal rim ommatidia.
A lobula tangential neuron whose cell body is located in the anterior dorsal area of the lateral cell body region. It forms varicosities in lobula layers 3, 4 and 5, and in the ventrolateral protocerebrum. It receives substantial synaptic input from Tm5a/b/c and Tm20 neurons, with a small number of synapses from each of a large number of Tm cells (Lin et al., 2016). There is only one neuron of this type per hemisphere.
Connectivity data was assessed by GRASP and double-labeling EM (Lin et al., 2016).
Glial cell that is part of the adult. Subtypes generally tend to tile, minimizing contact with their glial neighbors and maximizing contact with their neuronal compartment (Kremer et al., 2017). They also do not seem to recognize particular neurons or neuropils; sometimes one glial cell has partial coverage of multiple units and multiple glial cells may tile across the same unit (Kremer et al., 2017).
Glial cell that is part of the adult central nervous system.
Glial cell of the adult that is associated with the cell body rind of the brain. They have multiple lamelliform processes that intercalate in between neurons and wrap neuronal cell bodies (Hartenstein, 2011). They also wrap neuronal processes as they travel across the cell body rind (Kremer et al., 2017).
adult brain cortex associated glial cell
Glial cell of the adult that is associated with a neuropil of the brain. There are approximately 200 neuropil associated glial cells per hemisphere of the adult brain (Hartenstein, 2011).
Mesh-like structure composed of glial cells found in the cell body rind (cortex) of the adult brain (Awasaki et al., 2008). It is composed of cell body glial cells that locally elaborate and enwrap neuronal cell bodies (Awasaki et al., 2008).
Glial cell of the adult central nervous system that elaborates along the outer surface of its associated neuropil. Glia of this class may also surround neuropil bundles such as commissures or tracts. There are over 1000 of these in the adult central nervous system, some of which are descendants of larval ensheathing glia (Pogodalla et al., 2021).
adult ensheathing neuropil associated glial cell
adult fibrous lamellar neuropil associated glial cell
Neuropil associated glial cell of the central nervous system that has a dendritic morphology and elaborates inside the associated synaptic neuropil (Awasaki et al., 2008). Their nuclei are found at synaptic neuropil surfaces and they extend branched filiform or lamelliform processes that pervade the neuropil (Hartenstein, 2011). It expresses prospero, which specifies astrocyte-like, rather than ensheathing, fate in lineages that produce neuropil glia (Peco et al., 2016; Kato et al., 2020).
astrocyte-like neuropil associated glial cell
dendritic neuropil associated glial cell
reticular neuropil associated glial cell
reticular neuropil-associated glial cell
Glial cell that is in the process of becoming an adult satellite glial cell (Edwards et al., 2012). The two different populations of adult satellite glia arise from different larval precursors (Edwards et al., 2012).
Astrocyte-like (reticular) glial cell of the adult lamina (Edwards et al., 2012; Kremer et al., 2017). Each cell contributes to the wrapping of multiple columns and each column is wrapped by multiple glia (Edwards et al., 2012; Kremer et al., 2017). Epithelial glial cells elaborate numerous fine processes into the lamina plexus, especially from the surface juxtaposing the R1-R6 growth cones or axon termini (Poeck et al., 2001). In the lamina, they receive a small amount of synaptic input from each of photoreceptors R1-R6 and strong input from lamina intrinsic (amacrine) cells (Rivera-Alba et al., 2011). There are around 470 of these cells per lamina (Kremer et al., 2017).
Cell connectivity in the lamina was determined by analysis of semi-automated EM reconstruction of 749 serial sections of 21 complete lamina cartridges. The number of synaptic connections for a epithelial glial cell (presynaptic/postsynaptic) in a single lamina cartridge for each cell type was the following: R1 (-/15), R2 (-/13), R3 (-/7), R4 (-/9), R5 (-/10), R6 (-/11), Lai (-/87) (Rivera-Alba et al., 2011).
Epithelial glial cell of the embryo/larva.
Glial cell of the adult that is associated with the optic lobe.
Neuroblast that divides asymmetrically to regenerate itself and produce a smaller ganglion mother cell that generates two daughter neurons. Many of these neuroblasts switch to type 0 division at some point during their development, to produce daughters that develop into neurons with no further division (Baumgardt et al., 2014).
Bayraktar et al. (2010) show that type I neuroblasts can be distinguished from type II neuroblasts as being Deadpan-, Prospero- and Asense-positive.
Neuroblast that divides asymmetrically regenerate itself and produce a smaller intermediate neural progenitor (INP), which can produce multiple ganglion mother cells (Boone and Doe, 2008, Viktorin et al., 2011; Ren et al., 2016). Each type II neuroblast can produce multiple INPs, leading to the generation of multiple sublineages and typically more progeny than type I neuroblasts (Ren et al., 2016). It arises relatively late during embryonic development, delaminating from the dorsal cephalic neuroectoderm during stages 11-15 (Walsh and Doe, 2017). These cells and any existing INPs enter quiescence shortly before larval hatching (Walsh and Doe, 2017). There are eight type II neuroblasts per hemisphere, all belonging to the brain (Walsh and Doe, 2017).
Bayraktar et al. (2010) show that type II neuroblasts can be distinguished from type I neuroblasts as being Deadpan-positive, but Prospero- and Asense-negative. Walsh and Doe (2017) also use pointed as a positive marker. Arise later than NBs of embryonic NB map in Urbach and Technau (2003) - FBrf0173125 (Walsh and Doe, 2017).
Primordium of the late embryo that develops from the early primordium, and will give rise to the adult eye.
Transmedullary Tm5 neuron that is centered on a single yellow column in the medulla and arborizes in the M3, M6 and M8 layers, reaching some neighboring columns laterally (Kind et al., 2021). It selectively receives input from the R7 (and not R8) photoreceptor of its central column (Kind et al., 2021). Its axon terminates in lobula layer 5B after a characteristic reversal of direction (Kind et al., 2021). It provides input to the lobula intrinsic neuron Li4 via many synapses, and also to the lobula tangential neuron LT11 (Lin et al., 2016). It is a cholinergic neuron (Karuppudurai et al., 2014).
Connectivity in the medulla inferred from EM reconstructions (Gao et al., 2008; Kind et al., 2021). The neurotransmitter was assessed by immunohistochemistry (Karuppudurai et al., 2014). Connectivity in the lobula was assessed by GRASP and double-labeling EM (Lin et al., 2016).
Transmedullary Tm5 neuron that extends two or three vertical main dendritic branches in the medulla, spanning around five columns, from which branches spread laterally into layers M3, M6 and M8 (Kind et al., 2021). It receives most of its inner (R7/R8) photoreceptor input from the R7 photoreceptors of pale ommatidia (Kind et al., 2021). Its axon innervates lobula layer 5 (Kind et al., 2021). It provides input to the lobula intrinsic neuron Li4 via many synapses (Lin et al., 2016). It is a cholinergic neuron (Karuppudurai et al., 2014).
The neurotransmitter was assessed by immunohistochemistry (Karuppudurai et al., 2014). Connectivity in the lobula was assessed by GRASP and double-labeling EM (Lin et al., 2016). Photoreceptor input determined from EM (Kind et al., 2021).
Transmedullary Tm5 neuron that spans around eight medulla columns with lateral branches expanding out into the M1, M3 and M6 layers from a single vertical dendrite (Kind et al., 2021). It preferentially receives input from R8 (rather than R7) photoreceptor cells, and in most, but not all, cases these cells are selective for yellow (rather than pale) ommatidia (Kind et al., 2021). Its R8 input is mainly in layer M3 and it also receives input from the distal medullary amacrine neuron Dm8 in layer M6 (Karuppudurai et al., 2014). Its axon terminates near the boundary between lobula layers 5 and 6, with some cells having a branch in layer 4 (Kind et al., 2021). It provides input to the lobula intrinsic neuron Li4 via many synapses (Lin et al., 2016). It is a glutamatergic neuron (Gao et al., 2008; Karuppudurai et al., 2014).
The neurotransmitter was assessed in cells labelled with a glutamate GAL4 driver P{GawB}vGlut[OK371] (FBti0076967) (Gao et al., 2008), RT-PCR and by immunohistochemistry (Karuppudurai et al., 2014). Connectivity inferred from GRASP experiments (Karuppudurai et al., 2014; Lin et al., 2016), from EM reconstructions (Kind et al., 2021) or from double-labeling EM (Lin et al., 2016).
Columnar interneuron of the optic lobe whose collaterals are restricted to a single optic column.
This definition follows Fischbach and Dittrich (1989) in classifying based on the extension of the collaterals. A narrow field columnar neuron is classified as columnar by Morante and Desplan (2008).
Columnar interneuron of the optic lobe whose collaterals extend over more than one optic column.
This definition follows Fischbach and Dittrich (1989) in classifying based on the extension of the collaterals. A wide-field columnar neuron is classified as non-columnar by Morante and Desplan (2008).
Region of the adult brain cell body rind that overlies the neuropil of the deutocerebrum.
The supraesophageal neuropils of the adult brain located above, around and partially below the esophagus, including the optic lobes. It excludes the gnathal ganglion. Developmentally, it comprises three fused neuromeres: protocerebrum, deutocerebrum, and tritocerebrum.
This term is related to what used to be called supraesophageal ganglion, and is now referred to as supraesophageal zone. The adult cerebral ganglion, together with the gnathal ganglia (GNG), denote regions that follow the segmental neuromeres of the brain (the 3 rostral and 3 caudal, respectively). These are distinguishable from supra- and subesophageal zones, as these refer to the neuropil masses above and below the esophagus and do not respect neuromere boundaries (Ito et al., 2014).
Neuropil mass above the esophagus in the adult brain. It is part of the cerebral ganglion.
This term refers to what used to be called supraesophageal ganglion. The new name, together with subesophageal zone, refer to the neuropil masses above and below the esophagus and do not respect neuromere boundaries. The terms cerebral ganglia (CRG) and gnathal ganglia (GNG), denote regions that follow the segmental neuromeres of the brain (the 3 rostral and 3 caudal, respectively) (Ito et al., 2014).
Neuropil mass below the esophagus in the adult brain. It encompasses the gnathal ganglion, the prow and the saddle.
This term refers to what used to be called subesophageal ganglion. The new name, together with supraesophageal zone, refer to the brain tissue below and above the esophagus and do not respect neuromere boundaries. The terms cerebral ganglia (CRG) and gnathal ganglia (GNG), denote the segmental neuromeres of the brain (the 3 rostral and 3 caudal, respectively) (Ito et al., 2014). Sterne et al. (2021) - FBrf0251280 define the SEZ as comprising GNG + TR.
Region of the adult brain cell body rind that overlies the neuropil of the optic lobe. It includes the regions that overlie the lamina, medulla, lobula and lobula plate.
The primordium of the adult anterior optic tubercle (AOTU) in the larval anterior protocerebrum, laterally adjacent to the vertical lobe of the mushroom body (Lovick et al., 2017). It is initially a small, homogenous, hemispherical domain containing the distal filopodia of afferent optic lobe interneurons and the proximal filopodia of DALcl1/2 dorsal hemilineages (Lovick et al., 2017). During metamorphosis, the different subcompartments of the adult AOTU become distinct (Lovick et al., 2017).
embryonic/larval anterior optic tubercle primordial
Region of the larval cell body rind that overlies the neuropil of the brain.
Distal sublayer of the medulla layer M6, proximal to layer M5. It is defined by the extent of the arborization of Dm8 neurons proximally.
In the literature there are two methods for describing spatial location of neurons in the visual system: distal-proximal (e.g. Fischbach and Dittrich, 1989), and lateral-medial (e.g. Ito et al., 2014), both meaning outer and inner, respectively, and refer to the distance of a structure along the visual pathway relative to the center of the brain. Currently we will adopt the classical 'distal-proximal'.
Interneuron that innervates only the adult wedge.
Neuron that innervates the ventrolateral protocerebrum region only.
intrinsic ventrolateral protocerebrum neuron
Neuron whose cell body lies in the cortex of the lobula. It arborizes over a large area of the lobula, mostly in layer 5 but with some branches in layer 4. It receives very strong synaptic input from Tm5a/b/c and Tm20 neurons (Lin et al., 2016). There are approximately 30 of these cells per hemisphere (Lin et al., 2016).
An extrinsic columnar neuron that innervates the medulla.
Subregion of the larval superior lateral protocerebrum (CPLd) that will give rise to the adult lateral horn. It is defined by the axonal arbors of the olfactory uniglomerular projection neurons.
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).
Sublayer of the lobula layer 5 that is most proximal to layer 6.
This layer was identified by Brp staining (Wu et al., 2016).
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).
The epidermis of the embryonic ventral trunk.
Ommatidial subtype with stochastic distribution throughout the retina making up about 70% of all non-dorsal margin ommatidia. This ommatidial subtype is specialized to detect longer wavelengths (far UV + green).
The yellow ommatidium expresses the far ultraviolet-specific opsin Rh4 (FBgn0003250) in photoreceptor R7 cells and the green-sensitive Rh6 (FBgn0019940) in photoreceptor R8 cells (Wernet and Desplan, 2004).
Ommatidial subtype with stochastic distribution throughout the retina, making up about 30% of all non-dorsal margin ommatidia. This ommatidial subtype is specialized to detect shorter wavelengths (near UV + blue) than yellow ommatidia.
The pale ommatidium expresses the near ultraviolet-specific opsin Rh3 (FBgn0003249) in photoreceptor R7 cells and the blue-sensitive Rh5 (FBgn0014019) in photoreceptor R8 cells (Wernet and Desplan, 2004).
Photoreceptor cell R8 that is part of a yellow ommatidium and expresses Rhodopsin 6 (Wernet and Desplan, 2004). It outputs to TM5c, mostly in layer M3 where it terminates, but also in M1-2 (Karuppudurai et al., 2014) and to Tm20, Mi1, Mi4 and some lamina monopolar neurons of the same column (Takemura et al., 2015). It also outputs onto photoreceptor cell R7 of the same column (Takemura et al., 2008; Takemura et al., 2015), mostly in M3 (Takemura et al., 2008).
Connectivity with TM5c inferred from GRASP experiments (Karuppudurai et al., 2014). Connectivity with R7, Mi1, Mi4, Tm20 and lamina monopolar neurons based on EM data (Takemura et al., 2008; Takemura et al., 2015). Assertion in Gao et al. (2008) - FBrf0206213 that (non-DRA) R8 is synapsed to Tm9 is not supported by EM data in Takemura et al. (2015).
photoreceptor cell R8 of yellow ommatidium
Photoreceptor cell R8 that is part of a pale ommatidium and expresses Rhodopsin 5 (Wernet and Desplan, 2004). It outputs to TM5c, mostly in layer M3 where it terminates, but also in M1-2 (Karuppudurai et al., 2014) and to Tm20, Mi1, Mi4 and some lamina monopolar neurons of the same column (Takemura et al., 2015). It also outputs onto photoreceptor cell R7 of the same column (Takemura et al., 2008; Takemura et al., 2015), mostly in M3 (Takemura et al., 2008).
photoreceptor cell R8 of pale ommatidium
Photoreceptor cell R7 that is part of a yellow ommatidium and expresses Rhodopsin 4 (Wernet and Desplan, 2004). It outputs to transmedullary neuron Tm5a (Gao et al., 2008; Karuppudurai et al., 2014) and to Dm8 neurons in medulla layer M6 (Gao et al., 2008; Sancer et al., 2019). It receives synaptic input from photoreceptor cell R8 of the same column (Takemura et al., 2008; Takemura et al., 2015), mostly in M3 (Takemura et al., 2008).
Connectivity with Tm5a inferred from EM reconstructions from a single medulla column (Gao et al., 2008) and selective arborization in yellow columns (Karuppudurai et al., 2014). Connectivity to Dm8 based on EM data (Gao et al., 2008). Connectivity with R8 based on EM data (Takemura et al., 2008; Takemura et al., 2015).
photoreceptor cell R7 of yellow ommatidium
Photoreceptor cell R7 that is part of a pale ommatidium and expresses Rhodopsin 3 (Wernet and Desplan, 2004). It outputs to Dm8 neurons in medulla layer M6 (Gao et al., 2008; Sancer et al., 2019). It receives synaptic input from photoreceptor cell R8 of the same column (Takemura et al., 2008; Takemura et al., 2015), mostly in M3 (Takemura et al., 2008).
Connectivity to Dm8 based on EM data (Gao et al., 2008). Connectivity with R8 based on EM data (Takemura et al., 2008; Takemura et al., 2015).
photoreceptor cell R7 of pale ommatidium
Anatomical entity which is part_of Drosophila melanogaster.
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.
A(n) anlage that develops into some denticle field primordium. It develops from some ventral epidermis primordium.
FlyBase miscellaneous controlled vocabulary term.
Term that describes an allele, balancer, group or publication.
Term that specifies the dataset component type.
A set of biological data from a single study. Corresponds to the NCBI bioproject, GEO series or SRA study.
Biological source material characterized by an experiment.
Quantitative or qualitative assessment of biological source material to measure some attribute.
The type of assay as characterized by its data content.
A quantitative method for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing.
The type of result as characterized by its data content.
A result that is produced from the detailed examination of data to come to some conclusion.
A descriptor that describes some aspect of a dataset.
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.
A method used to characterize the biological molecules isolated from a biosample.
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.
A result that groups individual cells into populations sharing a similar transcriptional profile.
A result that represents a population of cells sharing a similar transcriptional profile.
A method to prepare and sequence a library of cDNAs obtained from single cells.
A method that uses the Chromium platform from 10x Genomics to prepare and sequence a cDNA library.
The life of an individual of the species Drosophila melanogaster, from fertilization to death.
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).
The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell.
A temporal subdivision of a developmental process.
Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3).
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.
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.
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.
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.
Oogenesis stage during which follicle cell division ceases.
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.
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).
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.
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.
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.
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.
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.
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.
Innermost chorionic layer and endochorion begin to form in the anterior of the follicle.
Secretion of innermost chorionic layer and endochorion begins in the main follicle cells.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells.
Secretion of the exochorion begins and ends.
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.
Developmental stage that starts with ovulation, at the end of oogenesis, until the egg is fertilized by a sperm.
Developmental stage that starts with sperm entry until the first mitotic division of the zygote.
Life stage that begins with a fertilized egg, and finishes with hatching at the end of embryonic stage 17 (Campos-Ortega and Hartenstein, 1997).
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).
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).
The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
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).
The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
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).
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).
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).
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).
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).
Stages during which the germ band is extended - 9-12.
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation.
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).
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).
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).
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.).
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.
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).
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).
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).
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).
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).
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).
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).
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).
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.
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
The stage of the Drosophila life-cycle from eclosion to death.
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.
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.
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.
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).
Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C.
The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion.
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.
Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage.
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.
Third instar larva from the beginning of wandering to the beginning of puparium formation.
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.
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.
A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion.
Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion.
Temporal subdivision of adulthood in days post-eclosion.
The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying).
Temporal ordering number - 391. Should not be used to stage embryos whose development is at temperatures other than 25'C.
Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying).
Temporal ordering number - 392. Should not be used to stage embryos whose development is at temperatures other than 25'C.
Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying).
Temporal ordering number - 393. Should not be used to stage embryos whose development is at temperatures other than 25'C.
Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying).
Temporal ordering number - 394. Should not be used to stage embryos whose development is at temperatures other than 25'C.
The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut.
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).
The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents.
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).
third instar - partially cleared gut stage
The substage of the wandering third instar larval stage when the larva has cleared its gut contents.
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.
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.
The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3).
Life stage from the end of adult stage A3, when tanning is complete, to death.
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
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.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
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.
A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
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.
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.
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.
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.
specimen role
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, collecting a stone from a site
A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
Definition updated following discussion on 2024-10-07 OBI dev call.
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.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed.
OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process.
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site.
A material entity that is collected for potential use as an input upon which measurements or observations are performed.
GROUP: OBI Biomaterial Branch
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
A structural quality inhering in a bearer by virtue of the bearer's forming a bundle of aligned anatomical fibers, as of muscle or nerve.
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
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.
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.
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.
The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote.
This includes all organisms which are made up of cells, e.g. bacteria, plants and animals.
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).
Single-cell RNA-seq study of larval optic lobes
Dissociated cells from larval optic lobe
Single-cell RNA-seq of dissociated cells from larval optic lobe
Clustering analysis of dissociated cells from larval optic lobe
Clustering analysis of dissociated cells from larval optic lobe, medulla forming neuroblasts cluster
Clustering analysis of dissociated cells from larval optic lobe, optic neuroblasts cluster
Clustering analysis of dissociated cells from larval optic lobe, immature T neurons cluster
Clustering analysis of dissociated cells from larval optic lobe, immature distal medullary amacrine neurons cluster
Clustering analysis of dissociated cells from larval optic lobe, ganglion mother cells cluster
Clustering analysis of dissociated cells from larval optic lobe, lamina forming neuroblasts cluster
Clustering analysis of dissociated cells from larval optic lobe, optic lobe neuroepithelial cells cluster
Clustering analysis of dissociated cells from larval optic lobe, CNS glial cells cluster
Clustering analysis of dissociated cells from larval optic lobe, immature lobula columnar neurons cluster
Clustering analysis of dissociated cells from larval optic lobe, Mi1 neurons cluster
Clustering analysis of dissociated cells from larval optic lobe, immature transmedullary neurons cluster
Clustering analysis of dissociated cells from larval optic lobe, T1 neurons cluster
Clustering analysis of dissociated cells from larval optic lobe, immature optic lobe centrifugal columnar neurons cluster
Clustering analysis of dissociated cells from larval optic lobe, Tm9 neurons cluster