An ontology of Drosophila melanogaster scRNAseq data from a single dataset (FBlc0006361). 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 FBlc0006361
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
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
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
attached to part of
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
A relationship that holds via some process of localization
Do not use this relation directly. It is a grouping relation.
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
has target end location
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
results in transport to from or in
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
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
attached to (anatomical structure to anatomical structure)
attached to
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.
A relation that holds between elements of a musculoskeletal system or its analogs.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
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 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
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.
Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).
The head segments that develop posterior to the embryonic/larval mouth.
The main middle section of the insect body comprising three thoracic rings: the pro-, the meso- and the metathoraces which are more or less well fused and cask-like sometimes having on the upper lateral part one of two pairs of wings, while on the ventrolateral part each thoracic ring bears a pair of legs.
Any segment (FBbt:00000003) that is part of some thorax (FBbt:00000015).
The first (most anterior) segment of the thorax.
The second (middle) segment of the thorax.
The most posterior of the three tagma (FBbt:00000002).
Sixth most anterior segment of the abdomen.
Eleventh most anterior segment of the abdomen.
Dorsal portion of the eighth segment and all structures posterior to it (Pignoni et al., 1992).
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).
Embryonic collection of cells that will give rise to the metameric regions of the embryo, comprising precursors of the gnathal, thoracic and abdominal segments (Campos-Ortega and Hartenstein, 1997).
Contiguous region of early embryonic cells that will invaginate to form the mesoderm during gastrulation (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).
Dorsal region of the ectoderm. It forms parts of the larval epidermis and the tracheal system, with other parts of these contributed to by the lateral ectoderm (Stathopoulos and Newcomb, 2020).
The region of the ectoderm anterior to the cephalic furrow.
Region of the ectoderm found posterior to the dorsal, lateral and ventral regions of the ectoderm and anterior to the posterior endoderm (Stathopoulos and Newcomb, 2020). It forms the hindgut (Stathopoulos and Newcomb, 2020).
The posterior invagination of ectoderm that gives rise to part of the digestive system.
Cell that has as its part a cytoskeleton that allows for tight cell to cell contact and which has apical-basal cell polarity.
Innermost germ layer of the embryo (Campos-Ortega and Hartenstein, 1997). It is formed by the invagination of two anlagen, those of the anterior and posterior midgut (Campos-Ortega and Hartenstein, 1997).
Middle germ layer of the embryo (between ectoderm and endoderm) following gastrulation (Campos-Ortega and Hartenstein, 1997). Shortly after its formation, its cells undergo mitosis and it loses its regular epithelial architecture (Campos-Ortega and Hartenstein, 1997). In stage 9 it reorganizes into a regular monolayer of cuboidal cells that lines the ectoderm (Campos-Ortega and Hartenstein, 1997). At the end of stage 10 further cell divisions disrupt this structure and its cells reform into two layers in stage 11 (Campos-Ortega and Hartenstein, 1997). It finally splits up into separate cell masses in late stage 11 (Campos-Ortega and Hartenstein, 1997). Its derivatives include the muscles, heart and fat body (Campos-Ortega and Hartenstein, 1997).
Region of mesoderm of that forms a layer interior to the ectoderm of the germ band (Campos-Ortega and Hartenstein, 1997). Following its invagination during ventral furrow formation in stages 6 and 7, it remains a coherent structure with no morphologically apparent subdivisions, apart from transient metamery during stage 9, until stage 11 (Campos-Ortega and Hartenstein, 1997). Its cells divide following invagination and it loses its epithelial integrity, forming a monolayer of cuboidal cells by stage 9 (Campos-Ortega and Hartenstein, 1997). A further division happens during stage 10 leading to two distinct layers by stage 11 (Campos-Ortega and Hartenstein, 1997).
Outer layer of the trunk mesoderm that arises due to mitosis at the end of stage 10 (Campos-Ortega and Hartenstein, 1997). It will give rise to the segmentally-repeated body wall muscles and the fat body (Campos-Ortega and Hartenstein, 1997).
Inner layer of the trunk mesoderm that arises due to mitosis at the end of stage 10 (Campos-Ortega and Hartenstein, 1997). It will give rise to the visceral musculature of the trunk (Campos-Ortega and Hartenstein, 1997).
Metameric subdivision of the embryonic abdomen.
Tracheal system of the late embryo or larva. The three larval instars retain the same basic pattern of the tracheal system, but with increasing complexity of branch trachea. It is composed of ten tracheal metameres.
The sum of all the structures in the embryo that will develop into the embryonic/larval digestive system.
presumptive embryonic/larval digestive system
A(n) primordium that develops into some rectum primordium and some large intestine primordium and some small intestine primordium and some embryonic primordium of adult hindgut precursor. It develops from some inclusive hindgut primordium.
A(n) primordium that develops into some Malpighian tubule tip cell primordium and some Malpighian tubule main body primordium. It develops from some inclusive hindgut primordium.
Primordium of the dorsal closure embryo that give rise to the salivary gland imaginal ring which in turn develops into the adult salivary gland.
embryonic primordium of adult salivary gland
Region of cells of the early embryo that will invaginate from the posterior dorsal embryo during gastrulation to form the posterior part of the endoderm (Campos-Ortega and Hartenstein, 1997). It is a precursor to the posterior midgut (Campos-Ortega and Hartenstein, 1997).
Any muscle cell (FBbt:00005074) that is part of some larval somatic muscle (FBbt:00058297).
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.
Muscle cell of a muscle of the embryonic/larval intestinal tract. Circular and longitudinal fibers surround the entire intestinal tract, with the exception of the recurrent layer of the proventriculus. The circular fibers derive from a bilaterally symmetrical band of mesodermal cells extending continuously throughout most of the germ band. The longitudinal fibers derive from clusters of mesodermal cells which appear during stage 12 at the posterior end of the embryo and migrate anteriorly.
Muscle cell of the gonadal sheath muscle of the embryo or larva.
embryonic/larval gonadal sheath muscle cell
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.
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.
Region of the larval central nervous system posterior to the gnathal neuromeres (Clark et al., 2018; Eschbach and Zlatic, 2020; Miroschnikow et al., 2020). It consists of three thoracic neuromeres, eight abdominal neuromeres and a terminal plexus (Clark et al., 2018).
There is some inconsistency in the literature as to whether the larval gnathal ganglion is a part of the ventral nerve cord, many recent papers consider it to be a distinct region, so it is not included here.
The sum of all the structures in the embryo that will develop into the embryonic/larval peripheral nervous system.
presumptive embryonic/larval peripheral nervous system
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.
A cluster of embryonic precursors that will give rise to sensory organs in the late embryo and larva (Ghysen et al., 1986; Bodmer and Jan, 1987).
peripheral nervous system precursor cluster
Any embryonic dorsal sensory organ precursor cluster (FBbt:00059182) that is part of some thoracic segment (FBbt:00000016).
embryonic thoracic dorsal sensory organ precursor cluster
Any external sensory organ precursor cell (FBbt:00005164) that is part of some embryonic thoracic dorsal sensory organ precursor cluster (FBbt:00001140).
dorsal thoracic external sensory organ precursor cell
Any embryonic ventral sensory organ precursor cluster group (FBbt:00059198) that is part of some thoracic segment (FBbt:00000016).
embryonic thoracic ventral sensory organ precursor cluster group
Any external sensory organ precursor cell (FBbt:00005164) that is part of some embryonic thoracic ventral sensory organ precursor cluster group (FBbt:00001172).
ventral group thoracic external sensory organ precursor cell
Any embryonic dorsal sensory organ precursor cluster (FBbt:00059182) that is part of some abdominal segment (FBbt:00000021).
embryonic abdominal dorsal sensory organ precursor cluster
Any external sensory organ precursor cell (FBbt:00005164) that is part of some embryonic abdominal dorsal sensory organ precursor cluster (FBbt:00001190).
dorsal abdominal external sensory organ precursor cell
Any embryonic ventral sensory organ precursor cluster group (FBbt:00059198) that is part of some abdominal segment (FBbt:00000021).
embryonic abdominal ventral sensory organ precursor cluster group
Any external sensory organ precursor cell (FBbt:00005164) that is part of some embryonic abdominal ventral sensory organ precursor cluster group (FBbt:00001220).
ventral group abdominal external sensory organ precursor cell
A glial cell that is part of (either layer of) the perineurium at the surface of the central nervous system.
Glial cell of the central nervous system.
Glial cell that forms the subperineurial glial sheath. These cells are polyploid. They increase in size and ploidy as the nervous system grows during development (Kremer et al., 2017).
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 that is part of the peripheral nervous system.
Any neuron (FBbt:00005106) that has its soma located in some supraesophageal ganglion (FBbt:00003626).
Neuroblast that generates cells of the ventral nervous system, including interneurons, motor neurons and/or glial cells (Bossing et al., 1996). These neuroblasts derive from the ventral neurectoderm (Bossing et al., 1996).
neuroblast of ventral nerve cord primordium
Applies to neuroblasts at all stages of development.
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 of the embryo that will develop into a dorsal thoracic disc.
Any dorsal thoracic disc primordium (FBbt:00001653) that is part of some prothoracic segment (FBbt:00000017).
Any dorsal thoracic disc primordium (FBbt:00001653) that is part of some mesothoracic segment (FBbt:00000018).
dorsal mesothoracic disc specific anlage
Primordium of the embryo that will develop into a ventral thoracic (leg) disc.
Any ventral thoracic disc primordium (FBbt:00001657) that is part of some prothoracic segment (FBbt:00000017).
ventral prothoracic disc specific anlage
Any ventral thoracic disc primordium (FBbt:00001657) that is part of some mesothoracic segment (FBbt:00000018).
ventral mesothoracic disc specific anlage
Tubular system of the late embryo and larva through which hemolymph flows.
A contractile tube in the embryo/larva that extends from immediately behind the posterior commissure of T1 to the arthrodial membrane of A7, into which it inserts via two caudally directed muscles which connect to lateral apodemes in A8. Throughout its length, its lumen is enclosed by just two cardial cells. This single-cell thick layer of cardial cells is surrounded by a single-cell thick layer of pericardial cells, except in the posterior thorax. In this region, it is surrounded by lymph gland in the anterior thorax where it passes through the ring gland. The whole tube is attached to the anterior region of each abdominal segment boundary by alary muscles.
Blood cell of the embryo or larva that is involved in the cellular immune response.
A cluster of 4-9 larval oenocytes situated bilaterally in each of abdominal segments 1-7 in a space between the dorsoventral muscles and the body wall. Each cell group is closely associated with an 'abdominal lateral pentascolopidial chordotonal organ lch5' and is supplied by its own tracheal branch.
Any abdominal larval oenocyte group (FBbt:00001695) that is part of some abdominal segment 6 (FBbt:00000027).
Adipose system of the late embryo/larva.
Fully developed fat body of the late embryo (from stage 17 onward) or the larva. It is a bilateral, multilobed organ that extends the length of the insect (Butterworth et al., 1965). It is one cell thick and between one and ten cells wide (Butterworth et al., 1965). Large holes and clefts form during stage 17, giving the fat body its definitive larval form (Campos-Ortega and Hartenstein, 1997).
Endocrine system of the late embryo/larva.
The primordium that will form the embryonic/larval corpus allatum, a substructure of the embryonic/larval ring gland. It is a paired structure that becomes distinct in early dorsal closure between the head mesoderm and the epidermis of the gnathal segments. During dorsal closure the paired primordia move dorsally to meet and fuse above the cardioblasts of the developing aorta.
The corpora cardiaca precursor first appear during stage 10 as two pairs of head mesoderm cells between the roof of the stomodeum and the inner surface of the brain primordium that derive from the anterior lip of the ventral furrow. Between stages 11 and 15, these cells migrate posteriorly, gradually increasing in number. During stage 15, they fuse with the precursors of the corpus allatum from the gnathal mesoderm to form the ring gland.
The endocrine complex which consists of the corpus cardiacum and corpus allatum (Hartenstein, 2006; Lee et al., 2008).
This is the common part of the adult (CA, CC, HG) and larval (CA, CC, PG) ring glands, but terminology seems to be very rarely used for the larva - https://orcid.org/0000-0002-1373-1705.
A cluster that surrounds the aorta, dorsal to the esophagus. It is composed of the corpus allatum (CA), corpus cardiacum (CC) and the prothoracic gland in the larva and the CA, CC and hypocerebral ganglion in the adult (Hartenstein, 1993). In the larva it is found anterior to the brain (Dai and Gilbert, 1991). The gland migrates posteriorly during pupal stages and the larval prothoracic gland degenerates (Dai and Gilbert, 1991). In the adult it is found posterior to the brain, just anterior to the proventriculus (Nassel and Zandawala, 2020).
Component of the larval ring gland that is continuous with the corpus cardiacum at its ventroposterior end, encircles the aorta, and surrounds the medially-located corpus allatum at its dorsoanterior end (Dai and Gilbert, 1991; de Velasco et al., 2004; Nassel and Zandawala, 2020). It is composed of very few cells in the late embryo, but these increase in size and number during larval development (de Velasco et al., 2004). It produces ecdysone and is most active in the early wandering third instar (Dai and Gilbert, 1991; Nassel and Zandawala, 2020). During pupal development, its cells separate, shrink and degenerate and none are found attached to the adult corpus allatum or corpus cardiacum after eclosion (Dai and Gilbert, 1991).
Neurohemal organ found medially in the anterodorsal part of the larval ring gland, surrounded by cells of the prothoracic gland (Dai and Gilbert, 1991; de Velasco et al., 2004). It is composed of smaller cells than the prothoracic gland (Dai and Gilbert, 1991). It produces juvenile hormone (Dai and Gilbert, 1991; Hartenstein, 1993).
Region of the larval ring gland closest to the brain that forms a U-shape around the floor of the aorta (Dai and Gilbert, 1991; de Velasco et al., 2004). It is connected to the brain by the nervi corporis cardiaci, which carry axons of secretory neurons that release neuropeptides in this location (Dirksen et al., 2008). It produces Adipokinetic hormone (Lee and Park, 2004) and sequesters insulin-like peptides released by insulin secreting cells of the pars intercerebralis (Ghosh et al., 2022). These two hormones are packaged into the same secretory vesicles (Ghosh et al., 2022).
Organism during the period between hatching and prepupa formation.
Rudimentary larval abdominal segment that surrounds the anal opening.
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 is a precursor of dorsal thoracic structures of the adult.
Dorsal imaginal disc of the prothoracic segment that is the precursor of structures of the adult dorsal prothorax including the humerus.
Dorsal imaginal disc of the mesothorax. Precursor of dorsal mesothoracic structures of the adult including the postnotum, scutum, scutellum, wing, wing hinge and part of the notal pleura.
Imaginal disc that is a precursor of a leg (a ventral thoracic structure of the adult).
Imaginal disc of the ventral prothoracic segment. Precursor of structures of the adult ventral prothorax including the prothoracic (1st) leg.
Imaginal disc of the ventral mesothoracic segment. Precursor of structures of the adult ventral mesothorax including the mesothoracic (2nd) leg.
A progenitor cell found in the larval epidermis that produces the adult external abdomen. These cells are part of the larval epidermis, secrete cuticle and contribute to larval epithelial patterning. They can be distinguished from the larval epidermal cells due to their small size and the fact that they remain diploid (Martinez Arias, 1993).
One of several groups of histoblasts in the epidermis of the larval abdomen that gives rise to part of the adult external abdomen during metamorphosis.
One of two histoblast nests per abdominal hemisegment (found in A1-A7). It is located in a dorsal position in the epidermis of the larval abdomen.
Bilaterally-paired histoblast nest found in the epidermis of abdominal segments 1-7. This nest is found in an anterior dorsal position and contains approximately 15 cells.
anterior dorsal histoblast nest abdominal
Bilaterally-paired histoblast nest found in the epidermis of abdominal segment 6. This nest is found in an anterior dorsal position and contains approximately 15 cells.
anterior dorsal histoblast nest abdominal 6
Bilaterally-paired histoblast nest found in the epidermis of abdominal segments 1-7. This nest is found in a posterior dorsal position and contains approximately 6 cells.
posterior dorsal histoblast nest abdominal
Bilaterally-paired histoblast nest found in the epidermis of abdominal segment 6. This nest is found in a posterior dorsal position and contains approximately 6 cells.
posterior dorsal histoblast nest abdominal 6
A ring shaped structure in the larva that gives rise to part of the adult.
Ring of imaginal cells situated where the larval salivary glands join the salivary ducts, from which the adult salivary glands develop.
Ring of imaginal tissue located at the anterior region of the embryonic/larval hindgut, posterior to where the Malpighian tubules join the hindgut, from which the adult hindgut forms. The hindgut imaginal ring cells are densely clustered, appear immature and have little cytoplasm (Murakami and Shiotsuki, 2001).
Imaginal tissue of the larva from which the adult anus develops.
Y-shaped tube that carries the secretions from the salivary glands to the embryonic/larval mouth.
Anterior length of the salivary gland duct. Anteriorly it connects to the atrium of the foregut. Posteriorly it bifurcates into the ducts of the individual salivary glands (Skaer, 1993).
embryonic/larval salivary gland common duct
Posterior part of the embryonic/larval alimentary canal, composed of pylorus (anterior), ileum and rectum (posterior) (Cohen et al., 2020).
Posterior-most portion of the embryonic/larval alimentary canal, terminating in the anus.
Posterior opening of the embryonic/larval hindgut.
Malpighian tubule of the embryo/larva. The larval tubule is very similar to that of the adult, except that the initial segment of the anterior tubule is bigger in the larva.
Specialized cell of the embryonic/larval Malpighian tubules.
embryonic/larval specialised Malpighian tubule cell
larval specialized Malpighian tubule cell
embryonic/larval specialized Malpighian tubule cell
Tip cell of the embryonic/larval Malpighian tubule.
embryonic/larval Malpighian tubule tip cell
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
Nerve that innervates the supraesophageal ganglion.
Any neuron (FBbt:00005106) that has its soma located in some subesophageal zone (FBbt:00051068).
Nerve that innervates the subesophageal ganglion.
Any neuron (FBbt:00005106) that has its soma located in some thoracic segment (FBbt:00000016).
Any neuron (FBbt:00005106) that has its soma located in some prothoracic segment (FBbt:00000017).
Any neuron (FBbt:00005106) that has its soma located in some mesothoracic segment (FBbt:00000018).
Any neuron (FBbt:00005106) that has its soma located in some abdomen (FBbt:00000020).
Any neuron (FBbt:00005106) that has its soma located in some larval abdominal segment 6 (FBbt:00001753).
Any nerve (FBbt:00005105) that is part of some prothoracic segment (FBbt:00000017).
Any nerve (FBbt:00005105) that is part of some mesothoracic segment (FBbt:00000018).
Any nerve (FBbt:00005105) that is part of some abdomen (FBbt:00000020).
Any larval sensillum (FBbt:00007240) that is part of some prothoracic segment (FBbt:00000017).
Any larval sensillum (FBbt:00007240) that is part of some mesothoracic segment (FBbt:00000018).
Any Keilin organ (FBbt:00005198) that is part of some larval mesothoracic segment (FBbt:00001744).
Any sensillum (FBbt:00007152) that is part of some larval abdomen (FBbt:00001746).
Any larval sensillum (FBbt:00007240) that is part of some abdominal segment 11 (FBbt:00000032).
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.
Tracheal system of the adult. It retains the same basic pattern of the larval tracheal system, except for the presence of air sacs and the disappearance of the last tracheal segment. It is composed of nine tracheal metameres.
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.
The salivary gland of the adult. It consists of two slender long, unbranched epithelial tubes of secretory epithelium that taper to form narrow ducts at their anterior end, which join to an unpaired duct (FBbt:00003137) in the neck region. The common duct connects to the salivary canal which runs through the hypopharynx and opens at its tip into the labial groove. The posterior ends of the lobes of the gland extend straight through the thorax on either side of the ventriculus and end in compact blind coils in the base of the abdomen. A suspensory muscle (FBbt:00003542) is attached to the anterior end of each lobe, near the cardia. (Miller, 1950 pg 440-1, 451).
Posterior part of the of the adult alimentary canal, extending from the posterior end of the midgut, where the Malpighian tubules meet, to the rectum, including the rectal pouch and rectal papillae (Miller, 1950; Skaer, 1993; Demerec, 1994). It has a characteristic loop morphology that forms independently of the rotation of the genitalia (Gonzalez-Morales et al., 2015).
Posterior-most region of the adult hindgut. It consists of a broadly expanded rectal sac (rectal ampulla) that tapers posteriorly to the narrow rectum proper, terminating at the anus. Protruding from the walls into the lumen of the rectal sac are two pairs of conical rectal papillae.
Dorsal vessel of the adult. It extends from the sixth abdominal segment to the dorsal anterior region of the brain (Curtis et al., 1999). The anterior portion, which is devoid of ostia, is the aorta, whilst the posterior (caudal) region, which has ostia, forms the heart proper.
The caudal, pulsatile region of the adult dorsal vessel. It extends from the first to the sixth abdominal segment, lying just below the surface of the cuticle, and has four pairs of ostia (Curtis et al., 1999). It is supported along the midline of the body by a series of paired alary muscles, suspensory fibrils and a rudimentary dorsal diaphragm (Miller, 1950). The caudal end is closed and is attached to the 6th abdominal tergite and to the dorsal wall of the rectal sac. The wall of the heart consists of a single muscular layer containing circular striated fibers and scattered lateral nuclei. On the ventral side, an outer layer or longitudinal muscles extends the whole length except for the caudal end.
Fat body of the adult. It is composed of diploid cells derived from cell clusters in the larval body wall and from adepithelial cells of the imaginal discs (Hoshizaki et al., 1995; Musselman and Kuhnlein, 2018). It is composed of various unconnected adipose tissue depots throughout the body (Musselman and Kuhnlein, 2018).
Small, spindle-shaped adult muscle precursor cell that is distinct from, but closely apposed to, the surface of an imaginal disc epithelium.
Any adepithelial cell (FBbt:00003219) that is connected to some humeral disc (FBbt:00001777).
adepithelial cell of dorsal prothoracic disc
Adepithelial cell associated with the prothoracic leg imaginal disc.
adepithelial cell of ventral prothoracic disc
adepithelial cell of prothoracic leg disc
Adepithelial cell associated with the wing imaginal disc. There are approximately 10 of these cells per wing disc at the end of embryogenesis; they proliferate throughout the larval stages to reach up to 2,500 cells by the late third instar larval stage. They give rise to the direct and indirect flight muscles of the adult (Gunage et al., 2014).
adepithelial cell of dorsal mesothoracic disc
Adepithelial cell associated with the mesothoracic leg imaginal disc.
adepithelial cell of ventral mesothoracic disc
adepithelial cell of mesothoracic leg disc
Cell persisting from the embryonic stage that contributes to the adult musculature. During metamorphosis, myoblasts aggregate and fuse together to form the adult muscle either on the remnants of larval muscles or independently on the newly forming adult epidermis (Bate, 1993).
embryonic precursor cell of adult muscle
Any embryonic precursor cell of adult muscle (FBbt:00003232) that is part of some thoracic segment (FBbt:00000016).
An adult muscle precursor cell found in an abdominal segment. In each of embryonic segments A1-7, there are four main clusters of these cells (dorsal, dorso-lateral, lateral and ventral) (Bate, et al., 1991) that are associated with peripheral nerves (Bate, 1993) and, during late embryogenesis, are connected to each other by a network of fine filopodia (Figeac et al., 2010). During metamorphosis, they migrate along the nerves to the sites of muscle formation at the epidermal histoblast nests (Bate, 1993).
Any muscle cell (FBbt:00005074) that is part of some adult somatic muscle (FBbt:00058784).
Any muscle cell (FBbt:00005074) that is part of some adult somatic muscle of head (FBbt:00058785).
Any muscle cell (FBbt:00005074) that is part of some adult somatic muscle of thorax (FBbt:00058828).
Any muscle cell (FBbt:00005074) that is part of some somatic muscle of prothorax (FBbt:00058856).
Any muscle cell (FBbt:00005074) that is part of some somatic muscle of mesothorax (FBbt:00058880).
Any muscle cell (FBbt:00005074) that is part of some flight muscle (FBbt:00058881).
Any muscle cell (FBbt:00005074) that is part of some indirect flight muscle (FBbt:00058882).
Any muscle cell (FBbt:00005074) that is part of some adult somatic muscle of abdomen (FBbt:00058966).
Any muscle cell (FBbt:00005074) that is part of some male abdominal muscle (FBbt:00059016).
Muscle cell of a visceral muscle of the adult.
Cell that are part of the muscle fibers of the hindgut, the posterior part of the alimentary canal. It contains longitudinal and circular muscle fibers.
Muscle cell of a muscle of the adult that is associated with the heart.
Muscle cell of a bilateral adult heart muscle that is involved in modulation of the flow of hemolymph into the cardiac tube, and support of the dorsal vessel during locomotion.
Muscle cell of a muscle that is part of an adult gonadal sheath.
Any neuroblast (FBbt:00005146) that is part of some thoracic segment (FBbt:00000016).
Any neuroblast (FBbt:00005146) that is part of some abdominal segment (FBbt:00000021).
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).
Region of the central nervous system consisting of the neuromeres of the three gnathal segments; mandibular, maxillary and labial (Ito et al., 2014; Hartenstein et al., 2018). It is located beneath the esophagus (Ito et al., 2014; Hartenstein et al., 2018). In the early larva, the three segmental neuromeres can be clearly identified, but they become fused during development and their segmental organization is obscured in the adult (Hartenstein et al., 2018).
Adult tract connecting the brain to the ventral nerve cord (Ito et al., 2014; Court et al., 2020). It emerges from the posterior gnathal ganglion (Ito et al., 2014; Court et al., 2020) and consists of 4 bundles of neurites in two bilateral pairs (one dorsal pair, one ventral pair) (Power, 1948). It contains around 3700 axons (Phelps et al., 2021).
The region of the adult central nervous system posterior to the brain, containing all of the thoracic and abdominal neuromeres (Court et al., 2020). It exists as a single consolidated ganglion located in the ventral part of the thorax (Court et al., 2020). It is connected to the brain by descending and ascending neurons that pass through the neck connective (Court et al., 2020).
Motor neuron that innervates the indirect flight muscles.
Any neuron (FBbt:00005106) that is capable of some peptide secretion (GO:0002790).
Any sensillum (FBbt:00007152) that is part of some head (FBbt:00000004).
A(n) anlage that develops into some inclusive hindgut primordium. It develops from some hindgut anlage in statu nascendi.
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.
Any sensillum (FBbt:00007152) that is part of some adult thorax (FBbt:00003018).
Any adult sensillum (FBbt:00007239) that is part of some prothoracic segment (FBbt:00000017).
Any adult sensillum (FBbt:00007239) that is part of some mesothoracic segment (FBbt:00000018).
A region of integument whose external cuticular part is a hard, sclerotized plate.
The dorsal plate (sclerite) of an adult abdominal segment.
Structure connecting the head to the body, through which the esophagus, cervical connective, two salivary gland ducts, two tracheal trunks and two stomodeal nerves pass.
The external integumentary structures that make up the surface of the adult abdomen.
Any abdominal tergite (FBbt:00004476) that is part of some abdominal segment 6 (FBbt:00000027).
A division of the whole organism into specialized systems.
System comprising the internal and external anatomy required for production of gametes and fertilization. It is sexually dimorphic.
The organ of the reproductive system in which the germ cells reside.
Thin covering of the gonads, containing one or more epithelial layers and a muscle layer.
Any reproductive system (FBbt:00004857) that is part of some male organism (FBbt:00007004).
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.
Air-filled network of tracheae, opening to the exterior via spiracles and containing minute tracheoles where gaseous exchange between air and tissues occurs (Miller, 1950).
Epithelial cell of the tracheal epithelium.
Organ system comprising the alimentary canal and its associated organs, including the mouthparts, labellar and salivary glands and the Malpighian tubules (Miller, 1950).
The system of organs and cells involved in the excretion of waste products.
System that functions to circulate hemolymph throughout the body. It is an open circulatory system, consisting of the dorsal vessel, body cavity, accessory pulsatile organs and the hemolymph (Miller, 1950).
Blood cell of the circulatory system that is involved in the cellular immune response. It expresses Hemese, a pan-hemocyte marker (Tattikota et al., 2020).
The system of organs and cells involved in fat storage.
Collective term for the masses and sheets of adipose tissue that are distributed throughout the organism's body. The adult and larval fat bodies are composed of different cell lineages, but perform the same main function of fat storage (Musselman and Kuhnlein, 2018).
The fat body primordium after the gonadal sheath primordium splits from it during stage 14. By stage 15, the different primordia fuse to form a continuous layer (Hoshizaki et al., 1994). The precursor fat cells it contains continue differentiating until stage 17, when the primordium becomes the fat body proper (Campos-Ortega and Hartenstein, 1997).
Non-connected system of anatomical structures which have some endocrine function.
System of contractile somatic and visceral muscle fibers arranged in groups and layers (Miller, 1950).
Muscle cell of a muscle that moves the viscera, usually with a peristaltic or compressing function, and has only one or, commonly no attachment to the body wall. Visceral muscles differ from somatic muscles in several respects: adjacent fibers are held together by desmosomes, each fiber is uninucleate and the contractile material is not grouped into fibrils but packs the whole fiber. The visceral musculature comprises musculature of the intestine, reproductive system and circulatory system (Miller, 1950). The circular fibers derive from a bilaterally symmetrical band of mesodermal cells extending continuously throughout most of the germ band. The longitudinal fibers derive from clusters of mesodermal cells which appear during stage 12 at the posterior end of the embryo and migrate anteriorly.
It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however most visceral (and somatic) muscles in Drosophila are actually striated (Miller, 1950; Bate, 1993).
Muscle cell that serves to change the position of some part of the body. These cells are usually attached to the body wall. Fibers of somatic muscles are multinucleate, with the contractile material grouped into fibrils.
Somatic and visceral muscles appear striated (Miller, 1950).
Somatic, contractile cell that makes up a muscle. It is formed by several fusion events between fusion competent myoblasts and one founder cell.
In contrast to vertebrates, in Drosophila embryos and larva, each muscle is a single myotube (Maqbool and Jagla, 2007).
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).
Posterior region of the central nervous system containing the thoracic and abdominal neuromeres (Clark et al., 2018; Court et al., 2020). In the larva it is joined at its anterior end to the posterior gnathal ganglion (Eschbach and Zlatic, 2020). In the adult it is a separate entity, connected to the brain by the neck connective (Ito et al., 2014; Court et al., 2020).
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.
A neuron that sends movement impulses to the muscle system.
Any neuron (FBbt:00005106) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
Any neuron (FBbt:00005106) that is capable of some hormone secretion (GO:0046879).
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 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).
Any glial cell that is part of (either layer of) the perineurium, which surrounds the entire nervous system (Kremer et al., 2017).
Glial cell that forms part of the perineurial sheath forming the outer layer of the nervous system. These cells divide extensively to increase in number as the nervous system expands during development (Kremer et al., 2017).
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.
A sensillum of the ventral sensory cluster group of the embryonic/larval thorax whose external sensory structure consists of a cluster of three hairs. It is innervated by 5 dendrites.
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).
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' carrying 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).
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).
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).
An anterior part of the alimentary canal derived from the ectoderm. It is lined on its luminal side by a impermeable cuticle. The proventriculus (cardia) is located at the junction between the foregut and midgut.
Paired secretory organ connected to the atrium via the salivary duct. It is essentially composed of two cell types: cuboidal epithelial duct cells that form tubes connecting the secretory cells to the larval mouth; and secretory cells that synthesize and secrete high levels of protein (Andrew et al., 2000).
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 portion of the embryonic nervous system that is part of the thorax.
The portion of the embryonic nervous system that is part of the abdomen.
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 foregut in a stage 5 embryo that will give rise to the foregut anlage.
Anlage in statu nascendi of the hindgut in a stage 5 embryo that will give rise to the hindgut 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).
A(n) anlage that develops into some salivary gland duct primordium.
Contiguous region of early embryonic cells that will invaginate during gastrulation to form a region of the endoderm (Campos-Ortega and Hartenstein, 1997).
A(n) anlage that develops into some trunk mesoderm.
Any primordium (FBbt:00005495) that develops into is part of some anatomical entity (FBbt:10000000) that is part of some circulatory system (FBbt:00005057).
embryonic/larval circulatory system specific anlage
The primordium of the gonadal sheath. This arises from clusters of cells in parasegments 10, 11 and 12 of the dorsal branch of the fat body/gonad primordium which split off during stage 14 and then cluster around the germ cells.
embryonic leading edge cell specific anlage
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).
The primordium that will form the embryonic/larval prothoracic gland, a substructure of the embryonic/larval ring gland. It originates in the dorsal ectoderm of T1, from which it segregates during stage 15 to form bilateral clusters near the heart precursors. In late embryogenesis, it partially fuses with the corpus allatum.
A(n) primordium that develops into some embryonic posterior Malpighian tubule. It develops from some Malpighian tubule primordium.
A(n) primordium that develops into some embryonic Malpighian tubule tip cell. It develops from some Malpighian tubule primordium.
Malpighian tubule tip cell specific anlage
A(n) primordium that develops into some embryonic small intestine. It develops from some hindgut proper primordium.
A(n) primordium that develops into some embryonic large intestine. It develops from some hindgut proper primordium.
A(n) primordium that develops into some embryonic/larval rectum. It develops from some hindgut proper primordium.
Primordium of the late extended germ band embryo that will give rise to the embryonic precursor of the adult hindgut.
embryonic primordium of adult hindgut precursor
Primordium of the late extended germ band and dorsal closure embryo that will give rise to the embryonic precursor of the adult muscle.
embryonic primordium of adult muscle precursor
Primordium of the larval segmentally-repeated body wall musculature. It arises from the outer layer of the trunk mesoderm. During germ band shortening (stage 13), it segregates into loose segmental clusters. Within these clusters, muscle formation proceeds by fusion of fusion competent myoblasts to muscle founder cells. Formation of the embryonic/larval somatic musculature is complete by stage 17.
Primordium which develops into the fat body and gonadal sheath. The cells that comprise it are specified from stage 10 (Jemc, 2010), though the first morphological sign of its development comes during stage 11, when the outer of the two layers of the trunk mesoderm thickens medially to become 2-3 cells thick. Segmentally arranged groups of cells split off from inner most layer of this thickening, becoming sandwiched between the somatic muscle primordium and the circular visceral muscle primordium. By stage 13, these segmental clusters have fused into continuous columns on either side of the embryo. These bands split into dorsal and ventral subdivisions. A sub-population of cells in the dorsal subdivision in parasegments 10-12 split off to form the gonadal sheath primordium during stage 14-15. The other cells then form the fat body primordium proper.
A(n) primordium that develops into some hindgut proper primordium and some Malpighian tubule primordium. It develops from some hindgut anlage.
A(n) primordium that develops into some dorsal apodeme anlage and some oenocyte primordium and some dorsal trunk epidermis primordium and some embryonic leading edge cell primordium and some dorsal sensory complex primordium and some abdominal histoblast anlage. It develops from some dorsal ectoderm.
A(n) primordium that develops into some embryonic/larval salivary gland duct. It develops from some salivary gland duct anlage.
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.
Dorsal-most region of the trunk mesoderm that gives rise to the dorsal vessel (Campos-Ortega and Hartenstein, 1997). It forms a leading edge as the invaginated trunk mesoderm spreads from ventral to dorsal (Campos-Ortega and Hartenstein, 1997). The left and right regions eventually fuse at the dorsal midline and their cells differentiate into cardioblasts and pericardial cells (Campos-Ortega and Hartenstein, 1997).
A(n) primordium that develops into some dorsal sensory complex proper primordium and some peripheral nervous system precursor cluster and some prothoracic gland primordium. It develops from some dorsal epidermis primordium.
Primordium which is formed by the delamination of neuroblasts from the ventral neurogenic region. The first of five waves of delamination starts towards the end of embryonic stage 8. During stage 11, the mesectoderm loses contact with the outer surface and forms neuronal and glial precursors in the midline of this primordium.
Ventral region of the trunk ectoderm, which gives rise to the ventral epidermis and the central nervous system (Stathopoulos and Newcomb, 2020).
The posterior part of the endoderm from its invagination as part of the amnioproctodeal invagination during stage 7, until it becomes morphologically distinct from the hindgut primordium due to a epithelial-to-mesenchymal transition at the end of stage 10 (Reuter et al., 1993). This epithelial-to-mesenchymal transition is also the transition from posterior endoderm to posterior midgut primordium.
The sum of all the structures in the embryo that will develop into the embryonic/larval tracheal system. This corresponds to the tracheal primordia and their component tracheal branch primordia along with primordia of the spiracles.
presumptive embryonic/larval tracheal system
The sum of the primordia in the embryo that will contribute to the embryonic/larval salivary gland.
Posterior region of the embryonic gut, posterior to the embryonic midgut. It is divided into 3 domains: small and large intestine and rectum. Border cells separate these three regions.
Anterior and small domain of the embryonic hindgut, posterior to the midgut.
Middle and long domain of the embryonic hindgut, posterior to the small intestine.
Malpighian tubule of the embryo. By mid-embryogenesis when cell division ceases, a phase of tubule elongation starts, and the number of cells surrounding the lumen decreases from 6 to 10 to only 2.
Posterior Malpighian tubule of the embryo.
Specialized cell of the embryonic Malpighian tubules.
embryonic specialised Malpighian tubule cell
embryonic specialized Malpighian tubule cell
Tip cell of the embryonic Malpighian tubule. It persists throughout tubule elongation during stages 13-16 and contacts a specific target by the end of the process (Weavers and Skaer, 2013). It adopts a specialized morphology with the cell body projecting from the tubule tip on the end of a microtubule-enriched stalk (Weavers and Skaer, 2013). It can extend filopodia and lamellipodia to explore its environment and remains free of basement membrane (Weavers and Skaer, 2013).
Imaginal cell, set aside during embryonic development, that will give rise to the adult hindgut. These cells are found in two rings of the hindgut; immediately posterior to the ureters of the Malpighian tubules, and at the anus. These two rings grow out and eventually unite.
The sum of all the structures in the embryo that will develop into the embryonic/larval muscle system.
presumptive embryonic/larval muscle system
Any muscle cell (FBbt:00005074) that is part of some embryonic somatic muscle (FBbt:00059033).
Excretory system of the late embryo or larva.
Malpighian tubule of the adult. It is very similar to that of the larva, except that the initial segment of the anterior tubule is much smaller in the adult.
Specialized cell of the adult Malpighian tubules.
adult specialised Malpighian tubule cell
adult specialized Malpighian tubule cell
Tip cell of the adult Malpighian tubule. The tip cell of the adult anterior tubules makes contact with alary muscles of the heart, whereas the tip cell of the posterior tubules contacts the a9 hindgut visceral nerve on the surface of the hindgut.
Epidermis of the dorsal region of the embryo.
Dorsal halve of an embryonic apodeme. The discontinuity between dorsal and ventral halves is visible on a lateral view.
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.
Posterior-most portion of the alimentary canal, terminating in the anus.
Gland of the endocrine system from which neurosecretory substances are released into the hemolymph.
Plate or plates that surrounds the anus.
Epithelial tube with excretory and osmoregulatory roles connected, via a ureter, to the alimentary canal at the junction of the hindgut and midgut. At mid-embryogenesis, there are 6 to 10 cells encircling the lumen, whereas later on, after a phase of tubule elongation, only 2 cells encircle the lumen. There are two pairs of Malpighian tubules: one pair arises from the dorsal part of the hindgut and lies at the anterior end of the abdomen; the other pair arises from the ventral part of the hindgut and lies at the posterior end of the abdomen. Each pair shares a common ureter. The anterior pair is longer than the posterior pair.
Posterior Malpighian tubule that extends from the midgut hindgut border. It is formed from the ventral part of the hindgut. There is a pair of these that are connected to a common ureter that is on the midgut/hindgut border. The posterior tubules extend towards the tail of the embryo, with each tubule positioned on opposite sides within the body cavity. At the end of embryogenesis, the distal ends switch sides by crossing over the posterior region of the hindgut. In the mature tubules, the tip cell of the posterior tubules makes contact with the a9 abdominal visceral nerve. The posterior tubule pair is shorter than the posterior one.
Specialized cell of the Malpighian tubules. There are four different types: type I, type II, tip and tiny cell.
Other cell types are known to exist, but have yet not been identified (personal communication by Helen Skaer).
Cell at the distal tip of each Malpighian tubule. It is involved in tube elongation in embryogenesis by stimulating cell proliferation in neighboring cells and in positioning the tubules.
Neuroendocrine structure that forms part of the ring gland. In the embryo and larva it is found around the floor of the aorta, just anterior to the brain (Dai and Gilbert, 1991; de Velasco et al., 2004, Nassel and Zandawala, 2020). It migrates posteriorly during metamorphosis (Dai and Gilbert, 1991) and is found posterior to the brain, near the proventriculus, in the adult (Nassel and Zandawala, 2020). It produces Adipokinetic hormone from late embryo to adult stages (Lee and Park, 2004).
Neuroendocrine structure that forms part of the ring gland. In the embryo and larva it is found dorsal the aorta, anterior to the brain (Dai and Gilbert, 1991; de Velasco et al., 2004, Nassel and Zandawala, 2020). It migrates posteriorly during metamorphosis (Dai and Gilbert, 1991) and in the adult it is found posterior to the brain, dorsal to the corpus cardiacum (Nassel and Zandawala, 2020). It produces juvenile hormone (Dai and Gilbert, 1991; Hartenstein, 1993; Nassel and Zandawala, 2020).
Imaginal tissue that has a dorsal location.
Peripheral nervous system of the embryo or larva.
embryonic/larval peripheral nervous system
Any anatomical entity (FBbt:10000000) that develops from some somatic trunk mesoderm (FBbt:00000129).
Any somatic stem cell (FBbt:00007344) that is part of some gonad (FBbt:00004858).
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.
Gonochoristic organism that can produce male gametes.
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.
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).
The outermost cellular layer of the nervous system, probably of mesodermal origin (Hartenstein and Jan, 1992). This layer consists of glial cells, which participate in nutrient uptake and establish a first diffusion barrier (Limmer et al., 2014).
Evidence of mesodermal origin comes from the observation that embryos lacking mesoderm lack this cell layer and the overlying neural lamella (Edwards et al., 1993).
The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial glial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the subperineurial glial sheath (sometimes referred to as the perineurial sheath inner layer).
Some authors use this term only to refer to the double layer of cells covering the CNS (e.g. Hartenstein and Jan, 1992), while other authors use it more broadly to include the covering of nerves (e.g. Banerjee et al., 2006). This ontology uses the term in its broad sense. 'Blood-brain barrier' may refer to this (e.g. Limmer et al., 2014) or the subperineurial glial sheath alone (e.g. Morante et al., 2013).
Inner glial cell layer of the perineurium that is probably not derived from the mesoderm (Edwards et al., 1994). This layer form an ion permeability barrier, functionally similar to the endothelial cells of the mammalian blood-brain barrier (Limmer et al., 2014).
That the subperineurial glial cells do not derive from the mesoderm is suggested by Edwards et al. (1994), in which they show the presence of these cells in delta (FBgn0000463) mutant embryos. 'Blood-brain barrier' may refer to this (e.g. Morante et al., 2013) or the perineurium (e.g. Limmer et al., 2014), which includes this and the perineurial glial sheath.
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.
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.
A cluster of cells of various types which form a discrete structure with a largely bona fide boundary.
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 with an innervated external cuticular sensory structure consisting of one or more bipolar sensory neurons, and 3 support cells: a trichogen cell which makes the external cuticular sensory structure, a thecogen cell which makes the socket that holds the base of the external sensory structure and a tormogen cell which makes the cuticular matrix (cap) at the tip of the innervating dendrite(s).
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).
Any sensillum (FBbt:00007152) that is part of some larval thorax (FBbt:00001741).
Specialized structure that is found on the cuticle.
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).
A region of cuticle and its underlying epidermis.
A segmental subdivision of the integument of the whole animal.
Specialized structure that is found on the integument.
Region of integument with boundaries corresponding to those of a tagma.
A multi-nucleate cell having no internal boundaries between nuclei.
Any cell (FBbt:00007002) that is capable of has target end location some hormone secretion (GO:0046879) that has target end location some circulatory system (FBbt:00005057).
Group of sense organs, and the somas and dendrites of sensory neurons, located ventrally in a larval segment (Campos-Ortega and Hartenstein, 1997). It lies outside the ventrolateral and ventral muscles, beneath the ventral insertion of the lateral transverse muscles (Campos-Ortega and Hartenstein, 1997). It can be divided into two smaller clusters (ventral and ventral'), with the axons of neurons of each cluster following a different branch of the segmental nerve (Willams and Shepherd, 1999). The pattern of sense organs and neurons is highly similar in segments A1-7, and slightly modified in the thoracic segments (Campos-Ortega and Hartenstein, 1997).
embryonic/larval thoracic/abdominal ventral sensory cluster
larval thoracic/abdominal ventral sensory cluster
Terminal (A8-10) segments have substantially different morphology, such that no 'ventral cluster' is present as seen in more anterior segments.
Any larval ventral sensory cluster group (FBbt:00007295) that is part of some prothoracic segment (FBbt:00000017).
embryonic/larval prothoracic ventral sensory cluster group
larval prothoracic ventral sensory cluster group
Any larval ventral sensory cluster group (FBbt:00007295) that is part of some mesothoracic segment (FBbt:00000018).
embryonic/larval mesothoracic ventral sensory cluster group
larval mesothoracic ventral sensory cluster group
Any larval ventral sensory cluster group (FBbt:00007295) that is part of some anterior abdominal segment (FBbt:00052393).
embryonic/larval ventral sensory cluster of A1-7
larval ventral sensory cluster group of A1-7
The integument of the larval mesothoracic segment.
integument of larval mesothoracic segment
The integument of the larval prothoracic segment.
integument of larval prothoracic segment
The integument of the larval abdominal segments.
A cluster of sense organs in the integument or connected to it.
Any nerve (FBbt:00005105) that is part of some larval head (FBbt:00001730).
Any epithelial cell (FBbt:00000124) that is part of some epidermis (FBbt:00004993).
The part of some organism that is part of some specified segment.
The part of an organ system that is part of some specified tagma.
Stem cell that is a progenitor of somatic cells.
Any larval ventral sensory cluster group (FBbt:00007295) that is part of some thoracic segment (FBbt:00000016).
embryonic/larval T1-3 ventral sensory cluster group
embryonic/larval thoracic ventral sensory cluster group
larval T1-3 ventral sensory cluster group
larval thoracic ventral sensory cluster group
Any material anatomical entity (FBbt:00007016) that is capable of has target end location some hormone secretion (GO:0046879) that has target end location some circulatory system (FBbt:00005057).
Any neuron (FBbt:00005106) that is capable of has target end location some hormone secretion (GO:0046879) that has target end location some circulatory system (FBbt:00005057).
Any neuron (FBbt:00005106) that overlaps some prothoracic gland (FBbt:00001724).
Any neuron (FBbt:00005106) that is part of some larval nervous system (FBbt:00001911) and overlaps some embryonic/larval corpus allatum (FBbt:00001725).
embryonic/larval corpus allatum innervating neuron
Any neuron (FBbt:00005106) that is part of some larval nervous system (FBbt:00001911) and overlaps some embryonic/larval corpus cardiacum (FBbt:00001726).
embryonic/larval corpus cardiacum innervating neuron
The portion of the embryonic/larval nervous system that is part of the thorax.
nervous system of embryonic/larval thorax
The portion of the embryonic/larval nervous system that is part of the abdomen.
nervous system of embryonic/larval abdomen
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 apodeme (FBbt:00005091) that is part of some abdomen (FBbt:00000020).
One of the first seven larval abdominal segments (counting from anterior to posterior). Larval segments 1-7 have almost identical musculature, gross tracheal morphology and sensory organ types and distribution.
Any glial cell (FBbt:00005144) that is part of some central nervous system (FBbt:00005094) and is part of some perineurial glial sheath (FBbt:00007089).
perineurial surface associated glial cell
Glial cell of the embryonic/larval CNS subperineurial glial sheath. These cells are rich in septate junctions and are a principal component of the larval blood-brain-barrier (Edwards and Meinertzhagen, 2010). They derive from the mesoderm (Edwards et al., 1993). In the larval abdomen there are typically 8 (but sometimes 9) subperineural glial cells per abdominal hemineuromere (Ito et al., 1995).
embryonic/larval CNS subperineurial glial cell
Subperineurial glia lies beneath the outer surface of the ventral nerve cord. Its nuclei and cell bodies are round and flat. Cytoplasmic extensions sometimes extend a short distance into the underlying cortex and fill the space between the outermost neuronal cell bodies.
A group of trichomes covering a region of integument.
Larval motor neurons are generally named according to the muscle(s) they innervate, meaning that their soma location may be in the same segment (segmental nerve neurons), or the next anterior segment (intersegmental nerve neurons) than given in the motor neuron name.
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).
The secretory part of the adult salivary gland, located posterior to the left and right salivary gland ducts. It consists of an epithelial tube 5-10 cells around surrounded by a thin basement membrane. The cells are cuboidal cells with small basal nuclei and a single large vacuole which fills most of the cell.
Ventral region of the adult brain, consisting of the fused ganglia of the three gnathal neuromeres; mandibular, maxillary and labial (Ito et al., 2014). It is found beneath the esophagus in the ventral part of the subesophageal zone (Ito et al., 2014).
This term refers to what used to be called subesophageal ganglion (SOG). The new name, together with cerebral ganglia (CRG), denote the segmental neuromeres of the brain (the 3 caudal and 3 rostral, 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). The posterior part of the GNG also corresponds to part of the inferior ipsl of Otsuna and Ito (2006) and to the ventral part of the subesophageal ganglion (SOG) of Chiang et al. (2011) (Ito et al., 2014).
A(n) anlage that develops into some salivary gland common duct primordium. It develops from some salivary gland duct inclusive primordium.
Primordium of the dorsal closure embryo that will give rise to the salivary gland common duct.
Primordium of the late extended germ band embryo that will give rise to the embryonic primordium of the adult salivary gland.
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.
A(n) primordium that develops into some embryonic dorsal epidermis. It develops from some dorsal epidermis primordium.
Anlage of the embryonic dorsal apodeme in the late extended germ band embryo.
Primordium of the embryonic dorsal apodeme in the dorsal closure embryo.
A(n) primordium that develops into some histoblast. It develops from some abdominal histoblast anlage.
A(n) primordium that develops into some embryonic dorsal sensory organ precursor cluster. It develops from some dorsal sensory complex primordium.
dorsal sensory complex proper primordium
Primordium that develops into some component of the larval ring gland.
A(n) primordium that develops into some adult salivary gland anlage and some salivary gland common duct anlage. It develops from some ventral ectoderm.
salivary gland duct inclusive primordium
A 'whorl' of larval oenocyte precursors which forms transiently around each 'chordotonal precursor cell C1' during stage 11. It ceases to exist when these cells delaminate during stages 11 and 12.
A(n) anlage that develops into some abdominal histoblast primordium. It develops from some dorsal epidermis 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 posterior ectoderm (FBbt:00000122).
Any anatomical entity (FBbt:10000000) that develops from some ventral ectoderm (FBbt:00005558).
Any anatomical entity (FBbt:10000000) that develops from some endoderm (FBbt:00000125).
Any anatomical entity (FBbt:10000000) that develops from some posterior endoderm (FBbt:00005560).
Any anatomical entity (FBbt:10000000) that develops from some mesoderm (FBbt:00000126).
Any anatomical entity (FBbt:10000000) that develops from some trunk mesoderm (FBbt:00000128).
Any anatomical entity (FBbt:10000000) that develops from some visceral trunk mesoderm (FBbt:00000130).
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.
A cell that is the principal cell type of the fat body and is filled with lipid droplets.
Adult and larval fat cells are specifically marked by Lsp2 expression, with greater expression at the larval stage (Lazareva et al., 2007 - FBrf0192478; Chintapalli et al., 2007 - FBrf0200485; Armstrong et al., 2014 - FBrf0226784). There is also relatively high expression of ppl and apollp in adult and larval fat cells (Colombani et al., 2003 - FBrf0161991; Chintapalli et al., 2007; Brankatschk and Eaton, 2010 - FBrf0211445).
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).
A neuron that is born during the embryonic phase of neurogenesis. These have functions in the larva (Lacin and Truman, 2016) and may be remodeled during metamorphosis to function during the adult stage (Veverytsa and Allan, 2013). In the larva, neurons of the same primary lineage have stereotyped cell body positions, with later-born primary neurons positioned further from the neuropil, and they share 1-2 fascicles by which they enter the neuropil (Mark et al., 2021).
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.
Epithelial component of the gonadal sheath.
Any motor neuron (FBbt:00005123) that sends synaptic output to some flight muscle cell (FBbt:00003360).
Motor neuron of the adult that has persisted from the larva, usually with some remodeling (Banerjee et al., 2016).
Any neuron with a cell body in the head and a process in the cervical connective. There are approximately 350 of these on each side of the brain (Namiki et al., 2018).
Namiki et al. (2018) operationally define a descending neuron as having a cell body in the brain and a process in the cervical connective, however, they include one neuron with a cell body in the head, but not the brain. This term encompasses such neurons - https://orcid.org/0000-0002-1373-1705.
Adult descending neuron with a cell body in the gnathal ganglion.
descending neuron of the gnathal ganglion
Any neuron projection bundle that carries fibers through part of the ventral nerve cord of the adult.
neuron projection bundle of thoracico-abdominal ganglion
neuron projection bundle of ventral nervous system
neuron projection bundle of adult ventral nerve cord
Any neuron projection bundle that carries fibers through part of the ventral nerve cord of the larva.
neuron projection bundle of larval ventral nerve cord
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.
Region of the larval cell body rind that overlies the neuropil of the larval gnathal ganglion.
cell body rind of larval subesophageal ganglion
cell body rind of larval gnathal ganglion
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).
Adult brain excluding the optic lobes. This consists of the cerebrum and the gnathal ganglion.
Any sensory neuron that enters the larval central nervous system via an abdominal nerve. These neurons receive sensory input from internal and external sensory organs of the peripheral nervous system. They may respond to proprioceptive, tactile, nociceptive or other stimuli.
Neuron of the male that is not found in the female.
Any adult neuron with its cell body in the thorax or abdomen (including appendages and ventral nerve cord) that passes through the cervical connective to the brain.
Cluster of cells in the ventrolateral ectoderm in the embryonic thorax that will eventually give rise to a dorsal imaginal disc, a ventral (leg) imaginal disc and a Keilin organ in the larva. The three different cellular identities cannot be distinguished at stage 11, but can by stage 14. There is one per thoracic hemisegment (six total).
Anatomical entity of the male that is not found in the same form in the female. If there is a counterpart in the female, the male and female types are substantially different.
For example, the testis is male-specific since it is substantially different to the ovary, which may be considered to be the female-specific counterpart. A male wing is not substantially different to a female wing, so is not considered male-specific.
A closely associated cluster of three neuroendocrine glands of the late embryo or larva, located anterior to the brain and dorsal to the esophagus (de Velasco et al., 2004). It consists of the corpus cardiacum posteroventrally (closest to the brain), the prothoracic gland laterally (forming most of the ring gland) and the corpus allatum anterodorsally (furthest from the brain) (de Velasco et al., 2004). It is innervated by neurons of the nerve of the corpus cardiacum and the aorta passes through it (de Velasco et al., 2004).
Perineurial glial cell of the adult ventral nerve cord. These cells have a varied morphology, ranging from elongated to square-shaped, with orientation mostly along the medial-lateral axis (Kremer et al., 2017).
adult thoracico-abdominal ganglion perineurial glial cell
Perineurial glial cell of the peripheral nervous system. Each cell forms a narrow strip along the long axis of the nerve, without covering its entire circumference (Kremer et al., 2017).
adult peripheral nervous system perineurial glial cell
Subperineurial glial cell of the peripheral nervous system. These cells can individually form elongated tubes around small peripheral nerves, but larger nerves are enclosed by multiple subperineurial cells (Kremer et al., 2017).
adult peripheral nervous system subperineurial glial cell
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
Descending neuron of the larva with its soma in the brain and processes extending into the ventral nerve cord (Winding et al. (2023).
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
Glial cell located amongst neuronal cell bodies in the cortex of the embryonic/larval ventral nerve cord (VNC). In the early larva, there are around 4 cell body glia per hemineuromere (Ito et al., 1995), but they increase in number during later larval stages, particularly in thoracic and anterior abdominal segments (Coutinho-Budd et al., 2017). The nuclei and cell bodies of the VNC cell body glial cells have quite irregular shapes, and cytoplasmic protrusions fill the space between neighboring neuronal cell bodies (Ito et al., 1995), with no morphological stereotypy by VNC region (Coutinho-Budd et al., 2017). These cells are not found in the dorsal portion of the cell body rind, with neuronal somas instead being wrapped by ensheathing glia (Pogodalla et al., 2021).
The endocrine complex which consists of the larval corpus cardiacum and corpus allatum.
More often referred to in combination with the prothoracic gland as the 'ring gland'. The term 'retrocerebral complex' is more often used for adult anatomy.
Nerve that connects the corpus cardiacum to the brain (de Velasco et al., 2004; Dirksen et al., 2008; Mahishi and Huetteroth, 2019). These nerves contain the axons of neurosecretory cells of the central nervous system projecting to the ring gland and aorta (Hartenstein, 2006; de Velasco et al., 2007; Dirksen et al., 2008; Huckesfeld et al., 2021).
Region of the adult brain cell body rind that overlies the neuropil found in the subesophageal zone.
cell body rind of adult subesophageal zone
Fat cell of the adult fat body. These cells are derived from cells of the larval body wall and adepithelial cells associated with imaginal discs (Hoshizaki et al., 1995; Musselman and Kuhnlein, 2018). Fully-differentiated adult fat cells are found from around 3-4 days after eclosion (Aguila et al., 2007). Unlike the larval fat cells, they are diploid (Musselman and Kuhnlein, 2018).
Fat cell that, during larval development, is flat, polygonal and tightly associated with other fat cells in the larval fat body (Nelliot et al., 2006). They accumulate nutrient reserves to act as a reservoir to support the animal through the non-feeding period of development (Aguila et al., 2007). Unlike the adult fat cells, they are endoreplicative (Musselman and Kuhnlein, 2018). After pupation, the larval fat cells adopt a more rounded shape and detach from each other in an anterior to posterior wave, leaving free-floating larval fat cells (Nelliot et al., 2006). The dissociated larval fat cells persist into the newly-eclosed adult to provide a food source (Aguila et al., 2007).
Fat cell of the late embryo, larva or early pupa that is part of the mature larval fat body. These cells are flat, polygonal and tightly associated with one another in single-layer sheets (Nelliot et al., 2006). They accumulate nutrient reserves to act as a reservoir to support the animal through the non-feeding period of development (Aguila et al., 2007). There are approximately 2200 of these cells (Butterworth et al., 1988).
Precursor cell of the embryo that will develop into a larval fat cell. These can first be detected around stage 10 in segmentally-repeated clusters (primary clusters) in the eve-expressing domain of parasegments (PS) 4-9 and PS13, just ventral to the midgut visceral mesoderm (Riechmann et al., 1998). In PS10-12, gonadal precursors are instead found in this position (Riechmann et al., 1998). In PS13, precursor fat cells are also found in the dorsal mesoderm that would be occupied by heart and midgut precursors in other segments (Riechmann et al., 1998). Secondary clusters of precursors arise in two positions, directly posterior to, and ventral and anterior to, the primary cluster (or gonadal precursors) in PS4-13 (Riechmann et al., 1998). At the onset of germ band retraction, these cells begin to divide and form a continuous layer between the midgut visceral mesoderm and the somatic mesoderm, losing their segmental appearance (Riechmann et al., 1998). These cells do not accumulate lipids (Campos-Ortega and Hartenstein, 1997).
Earliest marker is srp (Sam et al., 1996).
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).
Subperineurial glial cell of the embryonic/larval peripheral nervous system. These cells form a layer around the peripheral nerves, below the layer formed by the perineurial glial cells (Freeman, 2015).
larval peripheral nervous system subperineurial glial cell
embryonic/larval PNS subperineurial glial cell
Any neuron (FBbt:00005106) that has characteristic some sexually dimorphic (PATO:0002451).
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'.
Ascending neuron of the larva, having its soma in the ventral nerve cord and processes extending into the brain (Winding et al. (2023).
Ignores directionality of information flow, similar to 'adult ascending neuron'. Excludes neurons that 'ascend' from the gnathal neuromeres.
Neuroblast that has serial homologues across multiple neuromeres. All neuroblasts of the ventral nerve cord and gnathal ganglia are segmentally-repeated (Urbach et al., 2016). Most neuroblasts of the tritocerebrum and some neuroblasts of the deutocerebrum also have serial homology to neuroblasts of more posterior segments (Urbach et al., 2016).
A neuroblast located in one of the three gnathal segments. These are all homologues of neuroblasts in the thoracic segments (Urbach et al., 2016). The development of neuroblasts in the mandibular segment is significantly delayed compared to more posterior segments (Urbach et al., 2016) and their primary lineages are smaller (Rickert et al., 2018).
Any neuron (FBbt:00005106) that sends synaptic output to some motor neuron (FBbt:00005123).
Any neuron (FBbt:00005106) that sends synaptic output to some adult motor neuron (FBbt:00048235).
Any neuron (FBbt:00005106) that sends synaptic output to some embryonic/larval motor neuron (FBbt:00007675).
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).
Larval neuron that has its soma in the central nervous system and projects through the nervus corporis cardiaci (Huckesfeld et al., 2021). It releases neuropeptide in the ring gland or aorta via non-synaptic dense core vesicles (Huckesfeld et al., 2021).
Any neuron (FBbt:00005106) that has its soma located in some gnathal ganglion (FBbt:00004013).
The integument of a larval thoracic segment.
Ventralmost cluster of sense organs and sensory neuron somas, located ventrally within the larval ventral sensory cluster group (Bodmer and Jan, 1987; Orgogozo and Grueber, 2005). Axons of neurons in this cluster in abdominal segments follow branch SNc of the segmental nerve (Willams and Shepherd, 1999).
Any larval ventral sensory cluster (FBbt:00052115) that is part of some thoracic segment (FBbt:00000016).
Any larval ventral sensory cluster (FBbt:00052115) that is part of some prothoracic segment (FBbt:00000017).
larval prothoracic ventral sensory cluster
Any larval ventral sensory cluster (FBbt:00052115) that is part of some mesothoracic segment (FBbt:00000018).
larval mesothoracic ventral sensory cluster
Any larval ventral sensory cluster (FBbt:00052115) that is part of some anterior abdominal segment (FBbt:00052393).
larval abdominal ventral sensory cluster
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.
One of abdominal segments 8-11 (Campos-Ortega and Hartenstein, 1997; Birkholz et al., 2013). These segments have different patterns of neuroblasts, neurons, musculature and sense organs to more anterior abdominal segments (Campos-Ortega and Hartenstein, 1997; Birkholz et al., 2013).
Terminal segment of the adult. These segments collectively contain the genitalia and analia (Rice et al., 2019; McQueen et al., 2022).
Any neuroblast (FBbt:00005146) that is part of some terminal segment (FBbt:00052388).
One of abdominal segments 1-7 (Campos-Ortega and Hartenstein, 1997; Birkholz et al., 2013). These segments have a relatively consistent pattern of neuroblasts, neurons, musculature and sense organs from one segment to the next (Campos-Ortega and Hartenstein, 1997; Birkholz et al., 2013).
Any anterior abdominal segment of the embryo.
Any anterior abdominal segment of the adult.
Neuroblast found in one of abdominal segments 1-7. The pattern of neuroblasts is the same in each of these segments in the embryo (Birkholz et al., 2013; Urbach et al., 2016; Rickert et al., 2018).
Any motor neuron that is born during the embryonic stage. It may persist into the adult stage, usually with some remodelling (Banerjee et al., 2016).
Precursor cell that can give rise to one or more sensory neurons and/or support cells of the periphery.
Any segmental subdivision of integument of the larva.
segmental subdivision of larval integument
Any segmental subdivision of integument of the adult.
segmental subdivision of adult integument
Neurosecretory neuron of the adult with a cell body in the subesophageal zone.
adult neurosecretory cell of subesophageal zone
Any neurosecretory neuron (FBbt:00005130) that has its soma located in some brain (FBbt:00005095).
Any neurosecretory cell of brain of the adult.
Any neurosecretory cell of brain of the larva.
Any nervus corporis cardiaci of the adult.
Any nervus corporis cardiaci of the larva.
The entire integument of adult abdominal segment 6.
The entire integument of a single adult abdominal segment.
Division of an organism along its anterior-posterior axis.
anterior-posterior subdivision of organism
A multicellular structure made of one or several myofibers associated with tendon cells that attach the myofiber(s) to the exoskeleton or other organs.
Hemocyte of the adult organism. These cells all arise during embryonic and larval development and persist through metamorphosis and adult life (Holz et al., 2003; Sanchez Bosch et al., 2019).
An adepithelial cell of the wing disc that gives rise to an indirect flight muscle cell in the adult. These cells are located around the wing hinge primordium in the wing disc. They are distinguished from other flight muscle precursor cells by their expression of vestigial and zfh1 (Gunage et al., 2014; Zappia et al., 2020).
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).
Any glial cell (FBbt:00005144) that is part of some adult nervous system (FBbt:00003559) and is part of some perineurial glial sheath (FBbt:00007089).
Any glial cell (FBbt:00005144) that is part of some larval nervous system (FBbt:00001911) and is part of some perineurial glial sheath (FBbt:00007089).
Any glial cell (FBbt:00005144) that is part of some peripheral nervous system (FBbt:00005098) and is part of some perineurial glial sheath (FBbt:00007089).
Any glial cell (FBbt:00005144) that is part of some adult nervous system (FBbt:00003559) and is part of some subperineurial glial sheath (FBbt:00007091).
Any glial cell (FBbt:00005144) that is part of some larval nervous system (FBbt:00001911) and is part of some subperineurial glial sheath (FBbt:00007091).
embryonic/larval subperineurial glial cell
Any glial cell (FBbt:00005144) that is part of some peripheral nervous system (FBbt:00005098) and is part of some subperineurial glial sheath (FBbt:00007091).
Any visceral muscle cell (FBbt:00005070) that is part of some foregut (FBbt:00005379).
A contractile tube located underneath the dorsal epidermis. It ensures the hemolymph circulates within the hemocoel, by letting the hemolymph enter the tube through lateral slits (ostia) in the posterior end and pumping it back into the hemocoel (Rotstein and Paululat, 2016).
Columnar epithelial cell of the adult salivary gland responsible for producing and secreting the saliva (Andrew et al., 2000). It expresses the salivary gland-specific transcription factor sage (Fox et al., 2013).
Somatic muscle of the late embryo (stage 17+) or larva that is part of the fully developed larval musculature.
A muscle attached to the inner surface of the adult body wall, extending between articulated or flexibly joined areas, that serves to move the parts of the exoskeleton.
Somatic muscle that is part of the adult head.
Somatic muscle that is part of the adult thorax.
Somatic muscle that is part of the prothorax.
Somatic muscle that is part of the mesothorax.
Muscle involved in the mechanism of flight. The indirect flight muscles are involved in the deformation of the thoracic terga that bear the wings but are not directly attached to the wing, whereas the direct flight muscles are attached directly to the wing and aid in fine control of its movement. These muscles derive from adepithelial cells associated with the wing disc (Sudarsan et al., 2001; Kozopas and Nusse, 2002).
Muscle involved in flight that is not directly attached to the wing base. It derives from an indirect flight muscle precursor cell of the wing disc (Sudarsan et al., 2001).
Somatic muscle that is part of the adult abdomen.
Abdominal skeletal muscle that is specific to males.
Somatic muscle of the embryo, found prior to the fully-formed larval muscle pattern visible at stage 17. At stage 12, myoblasts of the somatic musculature are found in the superficial layer of the mesoderm, these differentiate and fuse to form muscle fibers by the end of stage 13. Between stages 13 and 17, the muscle fibers insert at apodemes formed by the epidermis and stretch during dorsal closure and head involution.
Glial cell that is embedded in the epithelium of a leg disc (Tripathi and Irvine, 2022; Tse et al., 2022).
The part of the adult Drosophila organism that encompasses the whole body except the head (Li et al., 2022).
A cluster of sensory organ precursor cells located dorsally in an embryonic segment (Ghysen et al., 1986).
embryonic dorsal sensory organ precursor cluster
A group of sensory organ precursor cells located ventrally in an embryonic segment. It is divided into two smaller clusters called ventral and ventral' (Bodmer and Jan, 1987; Ghysen et al., 1986).
embryonic ventral sensory organ precursor cluster group
Ventralmost cluster of sensory organ precursor cells, located ventrally within the embryonic ventral sensory organ precursor cluster group (Bodmer and Jan, 1987; Ghysen et al., 1986).
embryonic ventral sensory organ precursor cluster
Any embryonic ventral sensory organ precursor cluster (FBbt:00059199) that is part of some embryonic abdominal segment (FBbt:00000172).
embryonic abdominal ventral sensory organ precursor cluster
Any embryonic ventral sensory organ precursor cluster (FBbt:00059199) that is part of some embryonic thoracic segment (FBbt:00000167).
embryonic thoracic ventral sensory organ precursor cluster
Any neuron that has its soma in the adult brain and fasciculates with the nervus corporis cardiaci towards the ring gland.
Any epithelial cell (FBbt:00000124) that is part of some adult salivary gland (FBbt:00003135).
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.
Any glial cell (FBbt:00005144) that is part of some adult ventral nerve cord cell body rind (FBbt:00111082).
Any neuron (FBbt:00005106) that has its soma located in some adult ventral nerve cord cell body rind (FBbt:00111082).
A(n) somatic cell that is part of a(n) ectoderm anlage.
A(n) somatic cell that is part of a(n) endoderm anlage.
A(n) somatic cell that is part of a(n) mesoderm anlage.
A(n) somatic cell that is part of a(n) trunk mesoderm anlage.
A(n) somatic cell that is part of a(n) ectoderm.
A(n) somatic cell that is part of a(n) endoderm.
A(n) somatic cell that is part of a(n) mesoderm.
A(n) somatic cell that is part of a(n) somatic trunk mesoderm.
A(n) somatic cell that is part of a(n) visceral trunk mesoderm.
A(n) somatic cell that is part of a(n) trunk mesoderm.
A(n) somatic cell that is part of a(n) cardiogenic mesoderm.
A(n) somatic cell that is part of a(n) embryonic terminal segment.
somatic cell of embryonic terminal segment
A(n) somatic cell that is part of a(n) stage 5 embryo.
A(n) somatic cell that is part of a(n) embryonic/larval hindgut.
somatic cell of embryonic/larval hindgut
A(n) somatic cell that is part of a(n) embryonic/larval salivary gland.
somatic cell of embryonic/larval salivary gland
A(n) somatic cell that is part of a(n) inclusive hindgut primordium.
somatic cell of inclusive hindgut primordium
A(n) somatic cell that is part of a(n) presumptive embryonic salivary gland.
somatic cell of presumptive embryonic salivary gland
A(n) somatic cell that is part of a(n) trunk ectoderm.
A(n) somatic cell that is part of a(n) dorsal ectoderm.
A(n) somatic cell that is part of a(n) anterior ectoderm.
A(n) somatic cell that is part of a(n) fat body/gonad primordium.
somatic cell of fat body/gonad primordium
A(n) somatic cell that is part of a(n) Malpighian tubule primordium.
somatic cell of Malpighian tubule primordium
A(n) somatic cell that is part of a(n) dorsal epidermis primordium.
somatic cell of dorsal epidermis primordium
Any epithelial cell (FBbt:00000124) that is part of some embryonic/larval hindgut (FBbt:00001891).
Region of the embryonic/larval central nervous system consisting of the neuromeres of the three gnathal segments; mandibular, maxillary and labial (Hartenstein et al., 2018). Compared to thoracic and abdominal neuromeres, the number and size of primary lineages are decreased in the labial neuromere, and decrease further in each successive anterior gnathal neuromere (Rickert et al., 2018). It is found in the subesophageal zone, between the tritocerebrum and the prothoracic neuromere (Hartenstein et al., 2018). It separates from the prothoracic neuromere during metamorphosis (Kendroud et al., 2018).
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 that overlies the neuropil of the gnathal ganglion.
cell body rind around the gnathal ganglion
cell body rind of adult gnathal ganglion
Any sensory neuron (FBbt:00005124) that has its soma located in some abdomen (FBbt:00000020).
Anatomical structure that has multiple cells as parts.
A subdivision of the gut along its long axis.
Structure that produces and releases a chemical secretion. Exocrine glands release to the surface of the body or into a lumen, whereas endocrine glands release into the circulation.
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.
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 that is associated with the surface of the adult brain.
adult brain surface associated glial cell
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
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).
Small, oblong-shaped glial cell that is part of the (outer) perineurial sheath layer on the surface of the adult brain. It is located on top of the basal glial cell layer that is composed of the subperineurial glial cells.
The perineurial glial cells develop post-embryonically, in a non-GCM manner, and are thus likely to function only in the blood-brain-barrier of the adult (Edwards and Meinertzhagen, 2010).
Glial cell of the subperineurial glial sheath in the adult brain. These cells are fairly uniform in morphology across the brain, having a large, square and thin shape, giving them a sheet-like appearance (Awasaki et al., 2008, Kremer et al., 2017). Some also have circular protrusions that cap neuronal cell bodies not fully enclosed by cell body glia (Kremer et al., 2017).
adult brain subperineurial surface associated glial cell
Glial cell of the perineurial glial sheath in the embryonic/larval CNS.
The perineurial glial cells develop post-embryonically (Edwards and Meinertzhagen, 2010).
embryonic/larval CNS perineurial glial cell
Glial cell of the embryonic/larval peripheral nervous system that ensheathes axons and dendrites. The perineurial layer of glial cell lie on top of the inner, subperineurial glial cells (Banerjee et al., 2006).
embryonic/larval PNS perineurial glial cell
Broadly expanded, thin walled sac-like structure that tapers posteriorly to the narrower rectum proper terminating at the anus, at the posterior end of the adult hindgut.
Adepithelial cell associated with a leg imaginal disc. This cell will give rise to the muscle cells of the adult leg (Broadie and Bate, 1991).
adepithelial cell of ventral thoracic disc
One of the six larval segments, starting from the second anterior segment (counting from anterior to posterior). Larval segments 2-7 have identical musculature, gross tracheal morphology and sensory organ types and distribution.
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 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.
Superficial layer of the adult ventral nerve cord, composed of glia and the cell bodies of neurons (soma).
adult thoracico-abdominal ganglion cell body rind
adult thoracico-abdominal ganglion cortex
adult ventral nervous system cell body rind
Region of the larval cell body rind that overlies the neuropil of the ventral nerve cord.
cell body rind of larval ventral nerve cord
Region of the larval cell body rind that overlies the neuropil of the brain.
Any Keilin organ (FBbt:00005198) that is part of some larval prothoracic segment (FBbt:00001743).
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).
Anlage that develops into the posterior ectoderm. It is found posterior to the dorsal, lateral and ventral regions of the ectoderm anlage and anterior to the posterior endoderm anlage at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
The epidermis of the embryonic ventral trunk.
Anatomical entity which is part_of Drosophila melanogaster.
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 method for quantifying the transcriptome of individual cells, in which transcripts isolated from single nuclei 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 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 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 the adult thorax
Dissociated cells from wild-type adult male thoraces
Single-nucleus RNA-seq of dissociated cells from wild-type adult male thoraces
Clustering analysis of dissociated cells from wild-type adult male thoraces
Clustering analysis of dissociated cells from wild-type adult male thoraces, muscle cells cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, VNC neurons cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, indirect flight muscle cells cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, fat cells cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, VNC perineurial glial cells cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, salivary gland secretory cells cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, tracheocytes cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, alary muscle cells cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, epithelial cells cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, VNC cell body glial cells cluster
Clustering analysis of dissociated cells from wild-type adult male thoraces, hemocytes cluster