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

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

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
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 process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded by
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, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
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 and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
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

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

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

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

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

x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
This is the transitive form of the develops from relation
develops from

develops into

'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
expressed in

mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of

c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of

Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to

p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input

Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from

inverse of has developmental contribution from
developmentally contributes to

Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by

developmentally succeeded by

y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
expresses

q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of

A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to

A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to

A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to

this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of

holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
genomically related to

An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of

has member is a mereological relation between a collection and an item.
has member

input of

x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving

x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to

x has the potential to develop into y iff x develops into y or if x is capable of developing into y
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.

Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage

x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

A relationship between a material entity and a process where the material entity has some causal role that influences the process

p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.

gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p

A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process

Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.

Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
is carrier of

A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
has synaptic IO in region

A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
receives synaptic input in region

A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
sends synaptic output to region

A 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

Any anatomical entity (FBbt:10000000) that develops from some germ layer (FBbt:00000110).

An individual member of the species Drosophila melanogaster.

One of the three main divisions of the whole organism formed from groups of segments.

One of the repeated divisions of the whole organism.

Anterior part of the organism, including mouthparts, some sensory structures and the brain.

Head segment derived from the second embryonic segment (between the labral and antennal segments). In the larva, this segment includes Bolwig's organ.
While classically this structure is not considered to be a segment, but rather to be the non-segmental acron - anterior to the first segment, this ontology follows Schmidt-Ott and colleagues (Schmidt-Ott et al., 1994, and Schmidt-Ott and Technau, 1992) in considering it to be the second segment (posterior to the labral segment in the segmenting embryo). This is based on relating gene expression in the early segmenting embryo to the effects of loss of function mutations of these genes on formation of larval head structures.

Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).

A segment that is anterior to the gnathal segments.

Anteriormost procephalic segment, anterior to the ocular segment. In the adult it bears the clypeo-labrum.

Segment anterior to the intercalary segment. In the adult it bears the antennae.

An organism that is undergoing embryogenesis (Campos-Ortega and Hartenstein, 1997). Embryogenesis begins with a fertilized egg, and finishes with hatching at the end of embryonic stage 17 (Campos-Ortega and Hartenstein, 1997).

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

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

Outermost germ layer of the embryo (Campos-Ortega and Hartenstein, 1997). It is formed from the ectoderm anlage, which includes the cells of the cellular blastoderm monolayer that do not invaginate during gastrulation (Campos-Ortega and Hartenstein, 1997).

The region of the ectoderm anterior to the cephalic furrow.

Primordium of the late extended germ band and closure embryo that gives rise to the embryonic/larval optic anlage. It corresponds to the middle region that develops from the visual primordium.

Apodeme that is part of the late embryo/larva. Apodemes are not a continuous structure, but are split into two halves. In the embryo, this break is visible laterally. In the larva, the dorsal and ventral halves in the thoracic and abdominal segments are staggered, with the dorsal part being posterior to the ventral one.

The sum of all the structures in the embryo that will develop into the embryonic/larval nervous system.
presumptive embryonic/larval nervous system

The sum of all the structures in the embryo that will develop into the embryonic/larval central nervous system.
presumptive embryonic/larval central nervous system

Region that gives rise to the neuroblasts of the central nervous system (Bossing et al., 1996). An anterior region (procephalic neurogenic region) gives rise to the brain and a posterior, ventral region (ventral neuroectoderm) gives rise to the ventral nerve cord and gnathal ganglia (Bossing et al., 1996).

Tissue which becomes morphologically distinct shortly after cephalic furrow formation as two strips of about 80 enlarged cells which extend dorso-ventrally on either side of the developing head. It gives rise to neuroblasts of the brain.

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

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.

Glial cell of the central nervous system.

Glial cell with a nucleus amongst the neuronal cell bodies in the cell body rind. It is irregularly shaped, with processes that enclose the neuronal cell bodies.
Glial cells associated with axonal tracts (such as those associated with nerve roots) are excluded from this class of glial cells (Ito et al., 1995). Modeled as 'part of' their 'cell body rind' regions, though in practice some cell body glia have small projections into the neuropil - https://orcid.org/0000-0002-1373-1705.

Glial cell located amongst neuronal cell bodies in the cell body rind of the embryonic/larval central nervous system.

Glial cell that is part of the peripheral nervous system.

Neuroblast of one of the three procephalic regions, protocerebrum, deutocerebrum and tritocerebrum, which form the supraesophageal ganglion of the brain (Urbach et al., 2003). These neuroblasts derive from the procephalic neurogenic region (Urbach et al., 2003).

A neuroblast located in the protocerebrum. None of these are serial homologues of neuroblasts found in the thoracic neuromeres (Urbach et al., 2016).
In the embryo, individual neuroblasts are named according to their position relative to major morphological features (cephalic furrow, invaginating foregut, dorsal and ventral midline, their relative position with respect to each other, their time of segregation and their expression of markers) (Urbach et al., 2003).

A neuroblast located in the deutocerebrum. Some of these are serial homologues of neuroblasts found in the thoracic neuromeres (Urbach et al., 2016).

Any neuron (FBbt:00005106) that has its soma located in some supraesophageal ganglion (FBbt:00003626).

Neuron that is part of the larval nervous system. Neurons with functional roles in the larva are born during the embryonic phase of neurogenesis and further neurons, with adult-specific roles, are born during the postembryonic phase, which begins during larval development (Lacin and Truman, 2016).
This includes immature secondary neurons that are found in the larva - https://orcid.org/0000-0002-1373-1705.

Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993).

Population of contiguous, morphologically distinct cells of the embryo that will proliferate to form an imaginal disc in the larva. During early embryogenesis the precursor is part of the epithelial sheet before segregating from the epithelial sheet by late embryogenesis (Cohen, 1993).

Primordium from which the eye-antennal disc develops.

Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis.

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

Imaginal disc that, in the adults, gives rise to the eye, antenna, head capsule (including all bristles and external membranes) and the maxillary palps (Cohen, 1993).
Figure 12 from Cohen (1993, Bate, Martinez Arias, 1993: 747--841) provides a fate map of the eye-antennal disc.

Anterior, bulbous portion of the eye-antennal disc that gives rise to the eye as well as contributing to the head capsule (Cohen, 1993).

Central nervous system of the embryo/larva.

Supraesophageal ganglion of the late embryo or larva, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019).
embryonic/larval supraesophageal complex
embryonic/larval supraesophageal ganglion

Region of the embryonic or larval brain that contains the neuroepithelial cells that will give rise to the adult optic lobe, and the larval optic neuropil that processes visual information in the larva.

Any larval sense organ (FBbt:00002639) that is part of some ocular segment (FBbt:00000005).
embryonic/larval ocular segment sensillum

Any larval sense organ (FBbt:00002639) that is part of some labral segment (FBbt:00000008).
embryonic/larval labral segment sense organ

Any larval sense organ (FBbt:00002639) that is part of some antennal segment (FBbt:00000009).
embryonic/larval antennal segment sensillum

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 pre-oral neuropils of the brain located above and some of it below the esophagus, comprising three fused ganglia (protocerebrum, deutocerebrum, and tritocerebrum) in the head.
In the adult, this region is referred to as cerebral ganglia (Ito et al., 2014).

The most anterior neuromere of the central nervous system, developing from neuroblasts of the labral and ocular segments (Urbach and Technau, 2003; Ito et al., 2014). The protocerebrum comprises many discrete neuropil regions including the central complex and mushroom bodies (Ito et al., 2014).
Urbach and Technau (2003) divide the protocerebrum into labral and ocular neuromeres.

Neuron of the central nervous system that arborizes exclusively within a given neuropil domain, ipsilaterally or bilaterally.

A synaptic neuropil domain containing dendrites of Kenyon cells and receiving sensory interneuron afferents, mainly from the antennal lobes (Ito et al., 2014; Saumweber et al., 2018). It is located on the posterior side of the brain, close to the cortex where the cell bodies of the Kenyon cells are located (Lee et al., 1999; Saumweber et al., 2018). The peduncle extends anteriorly from the calyx to the base of the lobes (Ito et al., 2014; Saumweber et al., 2018).

Intrinsic neuron of the mushroom body. They have tightly-packed cell bodies, situated in the rind above the calyx of the mushroom body (Ito et al., 1997). Four short fascicles, one per lineage, extend from the cell bodies of the Kenyon cells into the calyx (Ito et al., 1997). These 4 smaller fascicles converge in the calyx where they arborize and form pre- and post-synaptic terminals (Christiansen et al., 2011), with different Kenyon cells receiving input in different calyx regions/accessory calyces (Tanaka et al., 2008). They emerge from the calyx as a thick axon bundle referred to as the peduncle that bifurcates to innervate the dorsal and medial lobes of the mushroom body (Tanaka et al., 2008).
Pre-synaptic terminals were identified using two presynaptic markers (Brp and Dsyd-1) and post-synaptic terminals by labelling a subunit of the acetylcholine receptor (Dalpha7) in genetically labelled Kenyon cells (Christiansen et al., 2011).

A bundle of neuron projections of Kenyon cells, dense with synapses, that extends from the calyx of the mushroom body to the base of the mushroom body lobe system (Ito et al., 1997).

The mushroom body lobe system consists of a vertical (dorsal) branch and a medial branch. In the larva, there are only two lobes (one dorsal, one medial), but remodeling during the pupal stage results in five lobes (two dorsal, three medial) in the adult (Lee et al., 1999).

Neuromere of the antennal segment, located between the protocerebrum and tritocerebrum, connected to antennal nerve trunk (Urbach and Technau, 2003; Ito et al., 2014).

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).

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.

A division of the whole organism into specialized systems.

The organ system that forms the covering layer of the animal.

The outer non-living layer of the integumentary system that is secreted by the underlying epidermis.

Non-innervated projection of the cuticle around an actin-rich cellular process of an underlying epidermal cell.

Tissue composed of epithelial cells. It secretes and underlies the cuticle.

The organ system involved in the absorption of nutrients.

A cuticular ingrowth of the exoskeleton, sometimes only a peg, frequently ridge-like, and often serving as a muscle attachment site. Does not generally correspond to superficial invaginations.

All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.

Collective name for all the nerve centers and their connective in the insect's body. In the context of Drosophila refers to the part of the nervous system consisting of the brain and ventral ganglia.

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

The outer parts of the nervous system that perform sensory and motor functions.

Electrically active cell of the nervous system which has an axon and/or dendrite and which is synapsed with other cells and/or has other cells synapsed to it.

Any neuron (FBbt:00005106) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).

A neuron that is entirely confined to the central nervous system and is neither a sensory neuron nor a motor neuron.

Any of a number of aggregations of neurons, glial cells and their processes, and surrounded by a glial cell and connective tissue sheath (plural: ganglia).

Multi-cell component structure of the central nervous system consisting largely of neuron projections (tracts and synaptic neuropil domains) and associated glial cells. This corresponds to the part of the CNS that is enclosed by the cortex.

A segmental subdivision of the nervous system.

A supporting cell of the nervous system.

Progenitor cell that gives rise only to glial cells and not neurons (Hartenstein, 2011).

Precursor of the central nervous system that derives from the neurogenic region of the ectoderm or the mesectoderm (Doe, 1992; Schmid et al., 1999; Crews, 2019). It produces neurons and/or glia (Doe, 1992; Beckervordersandforth et al., 2008). Neuroblasts may also divide during adult life to regenerate the adult brain (Fernandez-Hernandez et al., 2013).
Adult neurogenesis demonstrated in the adult optic lobe in response to injury (Fernandez-Hernandez et al., 2013).

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).

Embryo prior to the formation of the syncitial blastoderm, shortly after nuclear cycle 9 (Foe and Alberts, 1983; Jaeger et al., 2012). This period lasts from fertilization to the end of embryonic stage 3 (Campos-Ortega and Hartenstein, 1997).

Nuclear divisions 1 and 2. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).

Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL).

Nuclear division 9. The cleavage nuclei complete there migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying).

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

A blastoderm embryo prior to cellularization (corresponds to embryonic stages 3 and 4).

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

Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees C: approximately 40 minutes (130-170 minutes after egg laying).

Embryo that is in the process of gastrulation (encompassing embryonic stages 6-8), during which complex morphogenetic movements result in the formation of the three germ layers; ectoderm, mesoderm and endoderm (Hartenstein, 1993).

Embryo during the dorsal closure stage, which corresponds to stages 13-15 (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997). Dorsal closure occurs by extension of the dorsal epidermal primordium on either side, leading to fusion at the dorsal midline (Campos-Ortega and Hartenstein, 1997).

A posterior part of the alimentary canal derived from the ectoderm. It extends anteriorly from close to the point of attachment of the Malpighian tubules to the anus. It is lined on its luminal side by an impermeable cuticle (Skaer, 1993).
Adult and larval hindguts express the transcription factor brachyenteron (Sawyer et al., 2017).

The sum of all the structures in the embryo that will develop into the embryonic/larval integumentary system.
presumptive embryonic/larval integumentary system

Integumentary system of the late embryo or larva.

Bundle of Kenyon cell projections that arises from the anterior end of the pedunculus and projects dorsally. It consists of two components: the alpha lobe and alpha' lobe.

A bundle of Kenyon cell projections that arises from the anterior end of the pedunculus and projects medially. It consists of three components: the beta lobe, beta' lobe and gamma lobe.

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 embryonic central brain in a stage 5 embryo. It will give rise to the central brain anlage.
procephalic ectoderm anlage in statu nascendi

Anlage in statu nascendi of the visual system in a stage 5 embryo that will give rise to the visual system anlage.

Population of contiguous cells, typically arranged in one plane, that is morphologically indistinct from surrounding cells, but already corresponds to a later organ/tissue and can be identified based on gene expression or lineage tracing (Tomancak et al., 2002; Hartenstein, 2004).

Cells of the early embryo that will become the ectoderm following gastrulation (Campos-Ortega and Hartenstein, 1997). It remains at the surface of the embryo as the endodermal and mesodermal anlagen invaginate (Campos-Ortega and Hartenstein, 1997).

Anlage of the visual system in the gastrula embryo that will give rise to the visual primordium.

Precursor structure that can be recognized based on its distinct morphology and will give rise to one or more differentiated structures (Tomancak et al., 2002; Hartenstein, 2004). It develops from an anlage and may contain smaller anlage and primordia that will produce substructures (Tomancak et al., 2002).

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

Early primordium of the late extended germ band and dorsal closure embryo that will give rise to the adult eye. It develops from the visual primordium.

A(n) primordium that develops into some denticle field anlage and some anal pad primordium and some embryonic ventral epidermis and some imaginal disc primordium and some ventral apodeme anlage and some ventral trunk epidermis primordium. It develops from some ventral neurectoderm.

Primordium of the embryonic central brain in the extended germ band and dorsal closure embryo.

Primordium that develops into a region of head epidermis.

Ventral region of the trunk ectoderm, which gives rise to the ventral epidermis and the central nervous system (Stathopoulos and Newcomb, 2020).

Brain of the embryo that excludes the optic lobes. It includes the protocerebrum, deutocerebrum and tritocerebrum.

Glial cell of the embryonic central brain.

Epidermal pouch in the embryonic head that incorporates the acron and dorsal regions of the head segments. It forms following the movement of the dorsal fold over the clypeolabrum and procephalic lobe.
Note - possible redundancy between primordium term and embryonic term. ds060616.

Epidermis of the ventral region of the embryo.

Ventral halve of an embryonic apodeme. The discontinuity between dorsal and ventral halves is visible on a lateral view.

Plate or plates that surrounds the anus.

Bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. The mushroom body is divided into: the calyx, which is closest to the cortex and receives sensory interneuron afferents; the pedunculus, which is a thick axon bundle extending from the calyx to the base of the lobes; and the mushroom body lobe system, which consists of a vertical branch and a medial branch, which have different structures at different life stages (Lee et al., 1999; Ito et al., 2014).
This term as defined in Ito et al. (2014) corresponds to both the mushroom body (MB) and calyx (Cal) of Chiang et al. (2011).

Visual organ of the larva. It consists of a dense cluster of 12 ciliated photoreceptor neurons located on either side of the midline in a dorsomedial position in the anterior region of the larva.
Location in ocular segment on basis of FBrf0075072.

Any sense organ (FBbt:00005155) that is part of some antennal segment (FBbt:00000009).

Epidermal pouch in the head of the embryo or larva.

Primordium of the late extended and dorsal closure embryo that gives rise to the larval Bolwig organ. It corresponds to the most posterior region that develops from the visual primordium.

Peripheral nervous system of the embryo or larva.
embryonic/larval peripheral nervous system

Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.

Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.

Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.

Portion of tissue, that consists of one or more layers of cells with distinct apical-basal polarity, connected to each other by cell junctions.

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.

Any glioblast (FBbt:00005145) that is part of some central brain primordium (FBbt:00005542).

A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.

Neuroblast that is the precursor to the Kenyon cells (Kunz et al., 2012). There are four of these per hemisphere and they each arise from a distinct neuroectodermal progenitor and produce morphologically distinct primary lineages (Kunz et al., 2012). They continue to divide from the embryonic to the late pupal stage (Lee et al., 1999; Kunz et al., 2012). All four produce largely identical lineages postembryonically (Ito et al., 2013; Yu et al., 2013), sequentially producing gamma, alpha'/beta' and alpha/beta Kenyon cells (Lee et al., 1999; Kunz et al., 2012). In the adult, each lineage remains distinct within the calyx and pedunculus, but the axons reorganize and intermingle within the lobes (Li et al., 2020).
See Ito et al. (2013) figure S1 for distinction between MBp1-4.

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.

Any neuron (FBbt:00005106) that is capable of some acetylcholine secretion, neurotransmission (GO:0014055).

Calyx of the larval mushroom body. It contains dendrites of the larval Kenyon cells (Masuda-Nakagawa et al., 2009; Saumweber et al., 2018). It is organized into around 34 glomeruli, each innervated by a single projection neuron (Masuda-Nakagawa et al., 2009).

Any neuron (FBbt:00005106) that is capable of some gamma-aminobutyric acid secretion, neurotransmission (GO:0061534).
Some GABAergic neurons express ChAT transcripts (and reporters) at low levels, but do not produce functional enzyme (Lacin et al., 2019 - FBrf0242251).

A cluster of cells of various types which form a discrete structure with a largely bona fide boundary.

Sensillum that is internal to the animal - i.e. having no part that is part of the cuticle.

Any sensillum (FBbt:00007152) that is part of some larval head (FBbt:00001730).

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).

Specialized structure that is found on the integument.

The part of some organism that is part of some specified segment.

Stem cell that is a progenitor of somatic cells.

A neuron that uses a biogenic amine as its neurotransmitter (Vomel and Wegener, 2008; Fuchs et al., 2014).
Strictly speaking, "aminergic" should refer to any type of amine being used as a neurotransmitter. However, the term is most commonly used to refer to biogenic amines only, which is the meaning we retain here. See https://github.com/geneontology/go-ontology/issues/21625.

Sense organ that is internal to the animal - i.e. having no part that is part of the cuticle.

An interneuron that innervates only the mushroom body.

Structure consisting of the embryonic/larval foregut, midgut and hindgut.

A group of trichomes covering a region of integument.

An anlage that is a precursor of some part of the adult optic lobe in the larva. It develops from the embryonic optic lobe primordium.

An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception.
Note - the relationship of this class to the nervous system is overlap. This allows for sense organ components that function in the transduction of sensory signals but that are not considered to be part of the nervous system to be part of sensory systems.

Any neuron (FBbt:00005106) that capable of part of some sensory perception (GO:0007600).

Mushroom body (MB) of the larva. It only has two lobes, medial and vertical, in contrast to the adult MB, which has five lobes (Lee et al., 1999). Both lobes are composed of gamma neurons, which are the only Kenyon cells (KCs) present in the newly hatched first instar (Kunz et al., 2012). MB neuroblasts continue to produce new KCs throughout the larval stages (Lee et al., 1999). These new KCs form layers in the larval MB peduncle and lobes, with four distinguishable layers present in the third instar (Kurusu et al., 2002). Three types of KCs can be identified in these layers: embryonic-born gamma type (surface layer), larval-born gamma type (outer and inner layers) and larval-born alpha'/beta' type (core layer) neurons (Kurusu et al., 2002). During the pupal stage, alpha/beta KCs are produced and the larval MB is remodeled into the adult MB (Lee et al., 1999).
The four layers in the pedunculus and lobes were identified by staining with a FasII antibody. The surface layer is partially FasII-negative, the outer and inner layers are FasII-positive and the core is FasII-negative (Selcho et al., 2009; Kurusu et al., 2002).

A(n) primordium that develops into some lateral head epidermis. It develops from some central brain anlage.

Anlage of the embryonic central brain in the gastrula embryo that will give rise to the central brain primordium.

Primordium of the ventral trunk epidermis of the late extended germ band and dorsal closure embryo that will give rise to the embryonic ventral trunk epidermis.

Primordium of the anal pad of the late extended germ band and dorsal closure embryo that will give rise to the embryonic anal pads.

Anlage of the ventral apodeme of the late extended germ band embryo that will give rise to the ventral apodeme primordium.

Primordium of the ventral apodeme of the dorsal closure embryo that will give rise to the ventral apodemes.

Primordium of the denticle field of the dorsal closure embryo that will give rise to the larval denticle fields.

Region of embryonic and larval ventral cuticle that displays denticle belts. It develops from the denticle field primordium.

Any anatomical entity (FBbt:10000000) that develops from some ectoderm (FBbt:00000111).

Any anatomical entity (FBbt:10000000) that develops from some anterior ectoderm (FBbt:00000119).

Any anatomical entity (FBbt:10000000) that develops from some ventral ectoderm (FBbt:00005558).

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 synapsing neuron projections.

Region of synaptic neuropil whose boundaries are largely discontinuities in the density of presynaptic terminals: high density in the synaptic neuropil domain, lower or zero density outside this region. These boundaries often correspond to a boundary with glial sheath, tract neuropil or cortex.

A closely associated group of synaptic neuropil domains.

Structure consisting of a simple epithelium surrounded by visceral muscles, nerves and tracheae. The gut is divided into foregut, midgut and hindgut regions, based on developmental origin.

Any group of similar imaginal cells, such as an imaginal disc, imaginal ring or imaginal island, or a precursor tissue that forms one of them. These tissues develop separately from other embryonic and larval tissues and they generate adult structures during metamorphosis.

An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of light.

Any neuron (FBbt:00005106) that capable of part of some sensory perception of light stimulus (GO:0050953).

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).

Region of the cell body rind overlying the larval mushroom body.

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

Glial cell located amongst neuronal cell bodies in the cortex of the embryonic/larval brain.
embryonic/larval brain cortex glial cell

Glial cell that has not differentiated into a stable specialist fate. These cells may be migratory and/or phagocytic (Edwards and Meinertzhagen, 2010; Shklyar et al., 2014).

Any synaptic neuropil (FBbt:00040005) that is part of some mushroom body (FBbt:00005801).

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

Neuropil mass above the esophagus (Ito et al., 2014). It is part of the cerebral (supraesophageal) ganglion (Ito et al., 2014).

Neuropil mass above the larval esophagus consisting of the protocerebral and deutocerebral neuromeres and part of the tritocerebrum.
This is analogous to the adult term based on Ito et al. (2014), reflecting location relative to the esophagus, rather than segmental identity.

Neuron of the central nervous system that has the majority of its inputs and outputs in close proximity within the same region of the neuropil. Some arbors may spread outside of the region, but without sufficient polarity to define the neuron as an input or output neuron.

Region of the larval cell body rind that overlies the neuropil of the larval deutocerebrum.

Region of the larval cell body rind that overlies the neuropil of the larval protocerebrum.

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 larva.

Glial cell of the embryo that has not yet reached its mature larval form. These cells may further divide (or die), migrate or extend processes prior to adopting their mature larval forms, positions and numbers (Ito et al., 1995).

anterior-posterior subdivision of organism

Any larval neuron (FBbt:00001446) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).

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 late embryonic or larval peripheral nervous system.
embryonic/larval peripheral nervous system neuron

Any glial cell that is found in an eye-antennal disc (Gonzalez-Blas et al., 2020).

A(n) somatic cell that is part of a(n) ectoderm anlage.

A(n) somatic cell that is part of a(n) ectoderm.

A(n) somatic cell that is part of a(n) stage 5 embryo.

A subdivision of the cell body rind of the central nervous system. It includes the neuronal cell bodies.
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.

Any neuron (FBbt:00005106) that is capable of some glutamate secretion, neurotransmission (GO:0061535).
Some glutamatergic neurons express ChAT transcripts (and reporters) at low levels, but do not produce functional enzyme (Lacin et al., 2019 - FBrf0242251).

Anatomical structure that has multiple cells as parts.

A subdivision of the gut along its long axis.

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.

Primordium of the late embryo that develops from the early primordium, and will give rise to the adult eye.

The medial lobe of the larval mushroom body. It is associated with appetitive memory (Eschbach et al., 2020).
At third instar, the medial lobe comprise three types of Kenyon cells: embryonic-born gamma neurons, larval-born gamma neurons and larval born alpha'/beta' neurons (Pauls et al., 2010).

The vertical lobe of the larval mushroom body (Pauls et al., 2010).
At third instar, the vertical lobe comprise three types of Kenyon cells: embryonic-born gamma neurons, larval-born gamma neurons and larval born alpha'/beta' neurons (Pauls et al., 2010).

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

Region of the larval cell body rind that overlies the neuropil of the brain.

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

Anlage that develops into the anterior ectoderm. It is found anterior to the dorsal, lateral and ventral regions of the ectoderm anlage and posterior to the anterior endoderm anlage at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).

The epidermis of the embryonic ventral trunk.

Anatomical entity which is part_of Drosophila melanogaster.

Primordium of the embryo that will give rise to the adult eye. It corresponds to the most anterior region that develops from the visual primordium.

A(n) anlage that develops into some denticle field primordium. It develops from some ventral epidermis primordium.

FlyBase miscellaneous controlled vocabulary term.

Term that describes an allele, balancer, group or publication.

Term that specifies the dataset component type.

A set of biological data from a single study. Corresponds to the NCBI bioproject, GEO series or SRA study.

Biological source material characterized by an experiment.

Quantitative or qualitative assessment of biological source material to measure some attribute.

The type of assay as characterized by its data content.

A quantitative method for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing.

The type of result as characterized by its data content.

A result that is produced from the detailed examination of data to come to some conclusion.

A descriptor that describes some aspect of a dataset.

Some characteristic of an assay pertaining to the methods involved in processing the biological source material or generating the raw output data of the assay.

A method used to characterize the biological molecules isolated from a biosample.

A method for quantifying the transcriptome of individual cells, in which transcripts isolated from single cells are subjected to high-throughput sequencing and mapping to a reference genome.

A result that groups individual cells into populations sharing a similar transcriptional profile.

A result that represents a population of cells sharing a similar transcriptional profile.

A method to prepare and sequence a library of cDNAs obtained from single cells.

A method that uses the Chromium platform from 10x Genomics to prepare and sequence a cDNA library.

The life of an individual of the species Drosophila melanogaster, from fertilization to death.

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

The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell.

A temporal subdivision of a developmental process.

Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3).

Oogenesis stage that begins when the cyst leaves the germarium (from this point the cyst is referred to as an egg chamber). During this stage, polyploidation of the nurse cells begins, they reach a ploidy of 8C, and follicle cells start to divide.

Oogenesis stage that begins when the oocyte chromosomes condense into a karyosome attached to a distinctive spherical structure known as an endobody. The oocyte nucleolus disappears completely. During this stage, nurse cell ploidy reaches 16C.

Oogenesis stage that begins when the nurse cells chromosomes become bulbous. Nurse cell chromosomes during this stage are polytene and reach a ploidy of 32C. The egg chamber is oval shaped.

Oogenesis stage that begins when nurse cell chromosomes are no longer bulbous - the association between homologs weakens so that these chromosomes no longer have a polytene structure. During this stage, posterior nurse cell nuclei have a higher ploidy (64C) than anterior ones.

Oogenesis stage during which follicle cell division ceases.

Oogenesis stage during which polyploidation and enlargement of follicle cells begins. Nurse cell ploidy ranges from 256C (anterior) to 512C (posterior) and the egg chamber gains an elongated shape.

Oogenesis stage which begins when yolk first appears in the oocyte. Follicle cell migration over the oocyte begins during this stage (although mostly occurs during stage 9).

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

Oogenesis stage that begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends with the beginning of nurse cell dumping.

Oogenesis stage which begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends when centripetal follicle migration begins. During this stage, the migrating border cells reach the oocyte. The oocyte is about 50% egg chamber length.

Oogenesis stage that begins when the centripetal follicle cells begin to migrate. As a result, the vitelline membrane extends into the opercular region. This stage ends when nurse cell dumping begins.

Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins. The dorsal appendages begin to form during this stage. This stage ends when dying nurse cells form an anterior cap to the oocyte.

Oogenesis stage that begins when dying nurse cells form an anterior cap to the oocyte. Shortly after this, nurse cell dumping and growth of the oocyte are complete. Elongation of the dorsal appendages and formation of the innermost chorionic layer and endochorion begins during this stage.

Innermost chorionic layer and endochorion begin to form in the anterior of the follicle.

Secretion of innermost chorionic layer and endochorion begins in the main follicle cells.

Formation of specialized endochorion structures in the anterior of the follicle: branches in the developing dorsal appendages; compact endochorion lacking the pillars seen in the rest of the follicle.

Oogenesis stage that begins when the micropyle begins to form. At the beginning of this stage, about 12-15 nurse cell nuclei remain at the anterior of the oocyte. By the end of this stage, none of these nuclei remain. Oocyte meiosis up to arrest at full metaphase I occurs during this stage.

Oogenesis stage during which 12-15 nurse cell nuclei remain at the anterior of the oocyte. At this stage, the oocyte nucleus has reached its maximum volume and its chromosomes are compressed into a 5-7 micrometer karyosome.
Temporal ordering number - 10210. An alternative division of stage 13 into two sub-stages, A and B, has been defined on the basis of chorion development (see FBrf0043885). This ontology uses an alternative subdivision based on nurse cell nucleus number and oocyte meiosis, as the former at least, is easier to score than chorion ultrastructure.

Oogenesis stage during which 9-11 nurse cell nuclei remain at the anterior of the oocyte. During this stage, the nuclear membrane of the oocyte nucleus disappears, indicating the start of meiotic pro-metaphase.
Temporal ordering number - 10220. An alternative division of stage 13 into two sub-stages, A and B, has been defined on the basis of chorion development (see FBrf0043885). This ontology uses an alternative subdivision based on nurse cell nucleus number and oocyte meiosis, as the former at least, is easier to score than chorion ultrastructure.

Oogenesis stage during which only 7-8 nurse cell nuclei remain at the anterior of the oocyte. At the beginning of this stage, oocyte chromosome bivalents separate from each other - indicating mid-prometaphase of oocyte meiosis.

Oogenesis stage during which only 5-6 nurse cell nuclei remain at the anterior of the oocyte. The oocyte nucleus is in late prometaphase:the bivalents arrange themselves in on the equatorial plane of the spindle; homologous centromeres are pulled towards the poles.

The last stage of oogenesis. This stage begins when no nurse cell nuclei remain at the anterior of the egg (chamber). Exochorion formation and secretion occurs during this stage. The dorsal appendages complete their elongation and the follicle cells die.

Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells.

Secretion of the exochorion begins and ends.

The stage of the Drosophila life-cycle from maturation of an egg to the end of fertilization. At the beginning of this stage, the nucleus is arrested in meiotic metaphase I. The completion of meiosis and the start of protein synthesis are triggered by ovulation. If the female has already mated, fertilization begins during meiosis.

Developmental stage that starts with ovulation, at the end of oogenesis, until the egg is fertilized by a sperm.

Developmental stage that starts with sperm entry until the first mitotic division of the zygote.

Life stage that begins with a fertilized egg, and finishes with hatching at the end of embryonic stage 17 (Campos-Ortega and Hartenstein, 1997).

Stage prior to the formation of the syncitial blastoderm, including the first 9 cell divisions and the migration of nuclei to the periphery (cortex) of the embryo (Foe and Alberts, 1983; Jaeger et al., 2012). This lasts from fertilization to embryonic stage 3 (Campos-Ortega and Hartenstein, 1997).

The embryonic stage that lasts from the end of fertilization to the end of the second nuclear division. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).

The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

Nuclear division 9. The cleavage nuclei complete their migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying).

The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.

Stage during which most of the nuclei are arranged as a monolayer at the cortex (periphery) of the embryo (Foe and Alberts, 1983; Jaeger et al., 2012). It begins shortly after completion of the ninth cleavage division and lasts until the onset of gastrulation, including cleavage cycles 10-14A (Foe and Alberts, 1983; Jaeger et al., 2012). This corresponds to embryonic stages 4 (syncitial blastoderm stage) and 5 (cellular blastoderm stage) (Campos-Ortega and Hartenstein, 1997).

Cellularization. Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees: approximately 40 minutes (130-170 minutes after egg laying).

Stage during which gastrulation occurs. During this stage, cells from the polar caps and the mid-ventral part of the blastoderm invaginate and ultimately generate the germ layers (Hartenstein, 1993). This encompasses embryonic stages 6-8 (Hartenstein, 1993).

Stage 6 begins when the ventral furrow becomes apparent, an event which is followed rapidly by the formation of the cephalic furrow. Stage 6 ends when the pole cells have adopted a dorsal (horizontal) position at the posterior. Duration at 25 degrees C: approximately 10 minutes (170-180 minutes after egg laying).

Stage 7 begins when the pole cells have adopted a dorsal (horizontal) position at the posterior. Invagination of the anterior and posterior midgut and hindgut follows. The 'discoid plate' that carries the pole cells forms a pocket. Transverse furrows (dorsal folds) form on the dorsal surface. This stage ends when the anterior wall of the amnioproctodeal invagination starts moving anteriorly and the pole cells are no longer visible externally. Duration at 25 degrees C: approximately 10 minutes (180-190 minutes after egg laying).

Stages during which the germ band is extended - 9-12.

Stage 8 starts with the rapid phase of germ band extension and ends with the beginning of mesodermal segmentation. By the end of this stage germ band extension has progressed to the point where the proctodeal opening is at about 60% egg length and the dorsal folds (transverse furrows) are no longer visible. Duration at 25 degrees C: approximately 30 minutes (190-220 minutes after egg laying).

Stage 9 begins when mesodermal segmentation becomes (transiently) visible, and ends with the appearance of the stomodeal invagination slightly ventral to the anterior pole. Duration at 25 degrees C: approximately 40 minutes (220-260 minutes after egg laying).

Stage 10 begins with the appearance of the stomodeal invagination, slightly ventral to the anterior pole. Periodic furrows appear in the embryonic epidermis around the middle of the stage. The germ band continues to extend, reaching its maximum extent of 75% egg length towards the end of the stage. The end of the stage is marked by the beginning of invagination of the tracheal placodes. Duration at 25 degrees : approximately 60 minutes (260-320 minutes after egg laying).

Stage 11 begins with the invagination of the tracheal placodes. Para-segmental furrow form and segment boundary furrows become deep folds. Within the head, gnathal protuberances become apparent. The end of this stage is signaled by the appearance of a distinct cleft at the posterior pole of the embryo, which becomes detached from the vitelline membrane. This marks the beginning of germ-band retraction. Duration at 25 degrees C: approximately 120 minutes (320-440 minutes after egg laying).

Germ band retraction. Stage 12 begins when germ-band retraction starts and ends when this process is complete so that the prospective anal plate occupies the posterior pole. During this stage the posterior and anterior midgut primordia meet and fuse and the tracheal pits fuse to form the tracheal tree. Duration at 25 degrees C: approximately 120 minutes (440-560 minutes after egg laying).

Stage 13 begins at the completion of germ-band retraction, when the prospective anal plate occupy the posterior pole. The dorsal ridge becomes apparent externally; the clypeolabrum retracts, leaving a triangular shaped gap at the anterior pole; the labium moves to the ventral midline. This stage ends when head involution begins. Duration at 25 degrees C: Approximately 60 minutes (560-620 minutes after egg laying).

Stage 14 begins with the initiation of head involution. Closure of the midgut around the yolk and dorsal closure continue. Dorsal closure is 80% complete by the end of this stage. This stage ends with the appearance of the second midgut constriction. Duration at 25 degrees C: approximately 60 minutes (620-680 minutes after egg laying).

Stage following germ band retraction, during which dorsal closure happens (Hartenstein, 1993). Dorsal closure occurs by extension of the dorsal epidermal primordium on either side, leading to fusion at the dorsal midline (Campos-Ortega and Hartenstein, 1997). This corresponds to embryonic stages 13-15 (Hartenstein, 1993; Campos-Ortega and Hartenstein, 1997).

Stage 15 begins with the appearance of the second midgut constriction. During this stage the 1st and 3rd midgut constrictions form, dorsal closure is completed, and epidermal segmentation is accomplished. This stage ends when the intersegmental grooves can be distinguished at mid-dorsal level. Duration at 25 degrees C: approximately 100 minutes (680-780 minutes after egg laying).

Stage 16 begins when the intersegmental grooves can be distinguished at mid-dorsal level, and ends when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. During this stage the ventral cord retracts to about 60% egg length. Duration at 25 degrees C: approximately 180 minutes (780-960 minutes after egg laying).

Stage 17 begins when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. It lasts until hatching of the embryo (approximately 24 hours after egg laying), during which time much terminal differentiation occurs, the tracheal tree fills with air, so becoming completely visible, and the ventral cord continues to retract. Duration at 25 degrees C: approximately 8 hours (16-24 hours after egg laying).

The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation.

The first larval instar begins at hatching and ends at the first larval molt. Anterior spiracles are not yet present; posterior spiracles have two openings each. Salivary glands are very small and all cells are uniform in size. Mouth hooks typically have one tooth. Duration at 25 degrees C: approximately 25 hours (24-49 hours after egg laying; 0-25 hours after hatching).

The second larval instar begins at the first larval molt and ends at the second larval molt. Larvae are actively feeding and crawling in the food. Distinct anterior spiracles are present as enlargements at the end of the tracheal trunk, but not open to the outside; posterior spiracles have three openings each, and four groups of small unbranched hairs. The salivary glands extend to the first abdominal segment, and have cells that are uniform in size. Mouth hooks typically have two or three teeth. Duration at 25 degrees C: approximately 23 hours (49-72 hours after egg laying; 25-48 hours after hatching).

The third larval instar begins at the second larval molt and ends at puparium formation. Anterior spiracles are open to the outside; posterior spiracles have three openings each, and four groups of large branched hairs. The salivary glands extend to the second abdominal segment, with cells larger in the posterior than in the anterior of the gland. Mouth hooks typically have 9-12 teeth. About 24 hours before pupariation (at 25 degree C), larvae stop feeding and climb away from their food. Duration at 25 degrees C: approximately 48 hours (72-120 hours after egg laying; 48-96 hours after hatching).

Third instar larva prior to the wandering stage (approximately the first 24 hours of the third instar larval stage under standard conditions at 25'C.).

Stage of the third larval instar during which the larva wanders out of the food and climbs. Under optimum conditions at 25'C, this occurs approximately 24 hours after the start of the third instar larval stage.

The prepupal stage begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C: approximately 12 hours. (120-132.2 hours after egg laying; 0-12.2 hours after puparium formation).

Extends from puparium formation through tanning of the pupal cuticle. Posterior spiracles and ridge between anterior spiracles tan orange. Wriggling stops completely. Puparium becomes brown to the unaided eye. Duration at 25 degrees C: approximately 20 minutes. (120-120.3 hours after egg laying; 0-0.3 hours after puparium formation).

Male gonads become less distinct. Oral armature stops moving permanently. Dorsal medial abdominal contractions stop. Gas bubble becomes visible within abdomen. Duration at 25 degrees C: approximately 100 minutes. (120.3-122 hours after egg laying; 0.3-2 hours after puparium formation).

Ridge of the operculum becomes distinct. Puparium begins to separate from underlying epidermis. Becomes positively buoyant. Duration at 25 degrees C: approximately 4 hours, 45 minutes. (122-126.75 hours after egg laying; 2-6.75 hours after puparium formation).

Prepupal stage P4 begins as the lateral trunk trachea become obscured and ends when the imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 5 hours, 30 minutes. (126.75-132.2 hours after egg laying; 6.75-12.2 hours after puparium formation).

Lateral trunk tracheae become obscured. Dorsal medial abdominal contractions occur. Everted leg and wing discs become visible. Bubble appears in posterior of puparium, displacing the pupa anteriorly; abdominal bubble disappears. Duration at 25 degrees C: approximately 5 hours, 15 minutes. (126.75-132 hours after egg laying; 6.75-12 hours after puparium formation).

Bubble is displaced to anterior end of the puparium, and pupa withdraws to the posterior end. Imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 12 minutes. (132-132.2 hours after egg laying; 12-12.2 hours after puparium formation).

The pupal stage starts once larval/pupal apolysis is complete as indicated by the expulsion of the larval armature. Early in this stage, the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. Duration at 25 degrees C: approximately 32 hours. (132.2-164.3 hours after egg laying; 12.2-44.3 hours after puparium formation).
Temporal ordering number - 570. DISAMBIGUATION: In Drosophila lab vernacular, the term 'pupal stage' is often used to refer to the entire period from formation of the puparium to eclosion. However, this does not correspond to the standard usage of 'pupal stage' for Cyclorrhaphous flies (for discussion see: FBrf0087128). Briefly: formation of the puparium (hardening of the larval cuticle) marks the beginning of the pre-pupal stage. The pupal stage begins following pupal/larval apolysis - detachment of the larval epidermis from the puparium. In Drosophila, the outward sign of the completion of apolysis is the eversion of the head and expulsion of the larval mouthparts (FBrf0036849). We use P-stage to refer to the stage from pupariation to eclosion, and restrict pupal stage to its standard usage.

Pupal stage P5 starts when the legs and wings reach full extension along the abdomen and ends as the Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 6 hours, 30 minutes. (132.2-138.7 hours after egg laying; 12.2-18.7 hours after puparium formation).

Legs and wings reach full extension along abdomen. Enlarged initial segments of anterior pair Malpighian tubules move from thorax into abdomen. Translucent patch that lacks adhering fat body cells becomes discernible in the middle of the eye region. Pair of white Malpighian tubules becomes visible dorsally in the abdomen. Duration at 25 degrees C: approximately 66 minutes. (132.2-133.3 hours after egg laying; 12.2-13.3 hours after puparium formation).

Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 5 hours, 25 minutes. (133.3-138.7 hours after egg laying; 13.3-18.7 hours after puparium formation).

Dark green 'yellow body' appears between the anterior ends of the two Malpighian tubule segments, mid-dorsally at the anterior of the abdomen. Duration at 25 degrees C: approximately 13 hours, 45 minutes. (138.7-152.4 hours after egg laying; 18.7-32.4 hours after puparium formation).

The 'yellow body' moves back between the Malpighian tubules. The transparent pupal cuticle separates from the underlying epidermis. Eye cup becomes yellow at its perimeter. Duration at 25 degrees C: approximately 12 hours. (152.4-164.3 hours after egg laying; 32.4-44.3 hours after puparium formation).

Pale yellow pigmentation spreads inwards across the eye. Eye color becomes bright yellow, then changes to amber. Duration at 25 degrees C: approximately 12 hours 20 minutes. (164.3-176.6 hours after egg laying; 44.3-56.6 hours after puparium formation).

Eye color darkens to deep amber, then becomes pale pink. Duration at 25 degrees C: approximately 18 hours. (176.6-194.5 hours after egg laying; 56.6-74.5 hours after puparium formation).

Eyes become bright red. Orbital and ocellar bristles and vibrissae darken. Duration at 25 degrees C: approximately 6 minutes. (194.5-194.6 hours after egg laying; 74.5-74.6 hours after puparium formation).

Thoracic bristles become visible, and the tips of the wings turn grey. Duration at 25 degrees C: approximately 2 hours. (194.6-196.6 hours after egg laying; 74.6-76.6 hours after puparium formation).

Dorsal thoracic microchaetes and macrochaetes become visible. Duration at 25 degrees C: approximately 80 minutes (194.6-195.5 hours after egg laying; 74.6-75.9 hours after puparium formation).

Tips of folded wings become grey. Duration at 25 degrees C: approximately 45 minutes (195.5-196.6 hours after egg laying; 75.9-76.6 hours after puparium formation).

Pharate adult stage P12 begins as the abdominal tergite bristles become visible, and ends as the wings darken to black. Duration at 25 degrees C: approximately 2 hours. (196.6-198.6 hours after egg laying; 76.6-78.6 hours after puparium formation).

Bristles of the abdominal tergites become visible, and the wings become grey. Duration at 25 degrees C: approximately 55 minutes. (196.6-197.5 hours after egg laying; 76.6-77.5 hours after puparium formation).

Sex combs darken in males. Wings darken to black. Duration at 25 degrees C: approximately 65 minutes. (197.5-198.6 hours after egg laying; 77.5-78.6 hours after puparium formation).

Tarsal bristles darken and claws become black. Duration at 25 degrees C: approximately 3 hours, 20 minutes. (198.6-201.9 hours after egg laying; 78.6-81.9 hours after puparium formation).

The meconium appears dorsally at the posterior tip of the abdomen. Duration at 25 degrees C: approximately 9 hours, 30 minutes (201.9-211.5 hours after egg laying; 81.9-91.5 hours after puparium formation).

Pharate adult stage P15 begins with the tanning of the tergites and ends with eclosion. Duration at 25 degrees C: approximately 8 hours, 30 minutes. (211.5-220 hours after egg laying; 91.5-100 hours after puparium formation).

Tanning of the tergites obscures the Malpighian tubules and the 'yellow body'. Legs begin to twitch; fly is able to walk if puparium is removed prematurely. Ptilinum expands by hydrostatic pressure, opening the operculum. Duration at 25 degrees C: approximately 8 hours, 6 minutes. (211.5-219.6 hours after egg laying; 91.5-99.6 hours after puparium formation).

Stage which starts when the operculum opens and ends when eclosion is completed. Duration at 25 degrees C: approximately 24 minutes. (219.6-220 hours after egg laying; 99.6-100 hours after puparium formation).

The stage of the Drosophila life-cycle from eclosion to death.

Newly eclosed adult stage. Animal free of pupal case. Runs rapidly to find site for wing expansion. Wings are folded back and black against a very pale abdomen.
Temporal ordering number - 785. The time at which eclosed flies settle down for wing expansion can vary greatly. If they fail to find a suitable site then expansion can be delayed by several hours.

Stage, shortly after eclosion, during which the wings expand. During wing expansion, the abdomen pulsates and the hind legs stroke the wings vigorously for several minutes at a time. The stage ends when the wings are folded down over the abdomen, which has become broader and shorter, and the wing cuticle has lost its folds. The stage lasts around 15 minutes at 25'C.

The developing adult after pupal-adult apolysis, i.e.- from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion. Duration at 25 degrees C: approximately 55.7 hours (164.3-220 hours after egg laying; 44.3-100 hours after puparium formation).

Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C.

The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion.
Temporal ordering number - 490. DISAMBIGUATION: In Drosophila lab vernacular, the term 'pupal stage' is often used to refer to the entire period from formation of the puparium to eclosion. However, this does not correspond to the standard usage of 'pupal stage' for cyclorrhaphous flies (for discussion see: FBrf0087128). Briefly: formation of the puparium (hardening of the larval cuticle) marks the beginning of the pre-pupal stage. The pupal stage begins following pupal/larval apolysis - detachment of the larval epidermis from the puparium. In Drosophila, the outward sign of the completion of apolysis is the eversion of the head an expulsion of the larval mouthparts (FBrf0036849). We use P-stage to refer to the stage from pupariation to eclosion, and restrict pupal stage to its standard usage.

Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage.

The anterior spiracles are fully everted, with 7-9 finger-like projections. The body shortens, withdrawing three apparent abdominal segments and the larva sticks to its substrate.

Third instar larva from the beginning of wandering to the beginning of puparium formation.

A biological process whose specific outcome is the progression of an integrated living unit (an anatomical structure or an entire organism) over time from an initial condition to a later condition.

A cycle of nuclear division during the embryogenesis of Drosophila melanogaster. The first 13 cycles are synchronous throughout the embryo and occur their timing relative to other developmental processes is invariant. Later nuclear division cycles are asynchronous across the embryo although may be more locally synchronized.

A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion.

Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion.

Temporal subdivision of adulthood in days post-eclosion.

The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying).
Temporal ordering number - 391. Should not be used to stage embryos whose development is at temperatures other than 25'C.

Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying).
Temporal ordering number - 392. Should not be used to stage embryos whose development is at temperatures other than 25'C.

Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying).
Temporal ordering number - 393. Should not be used to stage embryos whose development is at temperatures other than 25'C.

Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying).
Temporal ordering number - 394. Should not be used to stage embryos whose development is at temperatures other than 25'C.

The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut.
Temporal ordering number - 462. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with the same color guts (dark blue) as feeding larvae (Andres and Thummel, 1994). Larvae at this stage are in chromosomal puff stage 1 (Andres and Thummel, 1994).

The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents.
Temporal ordering number - 465. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with lighter colored guts (light blue) than feeding larvae (Andres and Thummel, 1994). Larvae at this stage are mainly in chromosomal puff stages 2-7 (Andres and Thummel, 1994).
third instar - partially cleared gut stage

The substage of the wandering third instar larval stage when the larva has cleared its gut contents.
Temporal ordering number - 467. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with guts lacking any blue stain (Andres and Thummel, 1994). Larvae at this stage are mainly in chromosomal puff stages 7-9 and pupate within 1-6 hours (Andres and Thummel, 1994.

The execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module.

The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3).

Life stage from the end of adult stage A3, when tanning is complete, to death.

Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process

liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
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
A planned process with the objective of collecting a specimen.
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 to obtain a material entity for potential use as an input during an investigation.

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

specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch

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 first instar larval brains upon starvation

Cells from first instar larval brain upon normal feeding condition

Single-cell RNA-seq of cells from first instar larval brain upon normal feeding condition

Clustering analysis of cells from first instar larval brain upon normal feeding condition

Clustering analysis of cells from first instar larval brain upon normal feeding condition, neurons cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, peptidergic neurons cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, cholinergic neurons cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, glial cells cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, neuroblasts cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, Kenyon cells cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, optic lobe neuroepithelial cells cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, glutamatergic neurons cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, GABAergic neurons cluster

Clustering analysis of cells from first instar larval brain upon normal feeding condition, aminergic neurons cluster