http://orcid.org/0000-0002-1373-1705 http://orcid.org/0000-0002-7073-9172 https://orcid.org/0000-0001-5948-3092 https://orcid.org/0000-0002-0027-0858 An ontology of Drosophila melanogaster developmental stages. FlyBase Developmental Ontology (FBdv) https://creativecommons.org/licenses/by/3.0/ * FBdv:$sequence(8,7000,10000)$ 05:07:2021 10:40 FlyBase_development_CV 1.2 2021-07-05 definition term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom 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 Term not to be used for direct annotation Term not to be used for direct manual annotation ChEMBL GO slim Aspergillus GO slim Candida GO slim ChEMBL GO slim Generic GO slim Metagenomics GO slim PIR GO slim Plant GO slim Fission yeast GO slim Yeast GO slim Prokaryotic GO subset Systematic synonym namespace-id-rule subset_property synonym_type_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope shorthand 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 BFO:0000050 external part_of part_of part of part of http://www.obofoundry.org/ro/#OBO_REL: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. 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 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 BFO:0000051 OBO_REL:has_part external relationship has_part has_part has part has part has_part 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 http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 OBO_REL:preceded_by relationship preceded_by preceded_by 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. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process FBdv:00018001 relationship substage_of substage_of Creating this relation as a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO. substage_of 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 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 http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function 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. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_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. quality of 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 enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition 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. disposition of A part of relation that applies only between occurents. RO:0002012 FlyBase_development_CV occurent_part_of occurent_part_of occurent part of occurent_part_of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland 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 David Osumi-Sutherland di 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 David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of RO:0002087 FlyBase_development_CV immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by David Osumi-Sutherland 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 David Osumi-Sutherland ends_at_start_of meets RO:0002090 FlyBase_development_CV ends_at_start_of ends_at_start_of X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) ends_at_start_of immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during RO:0002092 external happens_during happens_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 happens during David Osumi-Sutherland o overlaps RO:0002093 external ends_during ends_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 ends_during 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) RO:0002131 FlyBase_development_CV overlaps overlaps overlaps overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component 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 Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan This is the transitive form of the develops from relation develops from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) positively regulates 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. Chris Mungall has function realized in 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. Chris Mungall has function in capable of part of true Chris Mungall 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. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 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. Chris Mungall consumes 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 Chris Mungall has developmental contribution from inverse of has developmental contribution from Chris Mungall 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 false Chris Mungall 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 A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within Inverse of developmentally preceded by Chris Mungall developmentally succeeded by cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect 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 Chris Mungall inheres in part of characteristic of part of true A mereological relationship or a topological relationship Chris Mungall 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) Chris Mungall 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 particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall 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. Chris Mungall false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of has input Chris Mungall 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). Chris Mungall 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 Chris Mungall 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 Chris Mungall 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 Chris Mungall has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes 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. Chris Mungall 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 of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ Chris Mungall molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. has modifier Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates 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 Chris Mungall has part structure that is capable of 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. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process disposition A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity quality A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role function An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity anatomical entity biological entity The life of an individual of the species Drosophila melanogaster, from fertilization to death. FBdv_root:00000000 Drosophila life cycle FlyBase_development_CV FBdv:00000000 Drosophila life The life of an individual of the species Drosophila melanogaster, from fertilization to death. FBC:DOS A collective term for stages 1-4. FlyBase_development_CV FBdv:00000054 Temporal ordering number - 25. cleavage stage A collective term for stages 1-4. FBC:DOS A collective term for stages 11 and 12. FlyBase_development_CV FBdv:00004450 Temporal ordering number - 300. late extended germ band stage A collective term for stages 11 and 12. FBC:DOS GO:0048477 oogenesis stage FlyBase_development_CV FBdv:00004886 Temporal ordering number - 10000. oogenesis A temporal subdivision of a developmental process. djs93 2009-10-01T05:56:56Z FBdv:00007010 FlyBase_development_CV FBdv:00005259 developmental stage A temporal subdivision of a developmental process. FBC:DOS Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3). FlyBase_development_CV FBdv:00005261 Temporal ordering number - 10010. oogenesis stage S1 Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3). FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005262 Temporal ordering number - 10020. oogenesis stage S2 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005263 Temporal ordering number - 10030. oogenesis stage S3 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005264 Temporal ordering number - 10040. oogenesis stage S4 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005265 Temporal ordering number - 10050. oogenesis stage S5 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 Oogenesis stage during which follicle cell division ceases. FlyBase_development_CV FBdv:00005266 Temporal ordering number - 10060. oogenesis stage S6 Oogenesis stage during which follicle cell division ceases. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005267 Temporal ordering number - 10070. oogenesis stage S7 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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). FlyBase_development_CV FBdv:00005268 Temporal ordering number - 10080. oogenesis stage S8 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). FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005269 Temporal ordering number - 10090. oogenesis stage S9 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005270 Temporal ordering number - 10100. oogenesis stage S10 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005271 Temporal ordering number - 10110. oogenesis stage S10A 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 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. FlyBase_development_CV FBdv:00005272 Temporal ordering number - 10120. oogenesis stage S10B 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005273 Temporal ordering number - 10130. oogenesis stage S11 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0043885 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005274 Temporal ordering number - 10160. oogenesis stage S12 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. FlyBase:FBrf0021038 FlyBase:FBrf0034074 FlyBase:FBrf0043885 FlyBase:FBrf0064777 Innermost chorionic layer and endochorion begin to form in the anterior of the follicle. FlyBase_development_CV FBdv:00005275 Temporal ordering number - 10170. oogenesis stage S12A Innermost chorionic layer and endochorion begin to form in the anterior of the follicle. FlyBase:FBrf0043885 Secretion of innermost chorionic layer and endochorion begins in the main follicle cells. FlyBase_development_CV FBdv:00005276 Temporal ordering number - 10180. oogenesis stage S12B Secretion of innermost chorionic layer and endochorion begins in the main follicle cells. FlyBase:FBrf0043885 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. FlyBase_development_CV FBdv:00005277 Temporal ordering number - 10190. oogenesis stage S12C 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. FlyBase:FBrf0021038 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. FlyBase_development_CV FBdv:00005278 Temporal ordering number - 10200. oogenesis stage S13 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. FlyBase:FBrf0021038 FlyBase:FBrf0029744 FlyBase:FBrf0034074 FlyBase:FBrf0064777 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. FlyBase_development_CV FBdv:00005279 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 S13A 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. FlyBase:FBrf0029744 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. FlyBase_development_CV FBdv:00005280 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 S13B 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. FlyBase:FBrf0029744 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. FlyBase_development_CV FBdv:00005281 Temporal ordering number - 10230. oogenesis stage S13C 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. FlyBase:FBrf0029744 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. FlyBase_development_CV FBdv:00005282 Temporal ordering number - 10240. oogenesis stage S13D 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. FlyBase:FBrf0029744 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. FlyBase_development_CV FBdv:00005283 Temporal ordering number - 10260. oogenesis stage S14 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. FlyBase:FBrf0043885 Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells. FlyBase_development_CV FBdv:00005284 Temporal ordering number - 10270. oogenesis stage S14A Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells. FlyBase:FBrf0021038 FlyBase:FBrf0043885 Secretion of the exochorion begins and ends. FlyBase_development_CV FBdv:00005285 Temporal ordering number - 10280. oogenesis stage S14B Secretion of the exochorion begins and ends. FlyBase:FBrf0021038 FlyBase:FBrf0043885 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. FlyBase_development_CV FBdv:00005286 Temporal ordering number - 10290. egg stage 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. FlyBase:FBrf0064779 FlyBase_development_CV FBdv:00005287 Temporal ordering number - 10300. unfertilized egg stage FlyBase_development_CV FBdv:00005288 Temporal ordering number - 10. fertilized egg stage The stage of the Drosophila life-cycle from fertilization to hatching. FlyBase_development_CV FBdv:00005289 Temporal ordering number - 20. embryonic stage The stage of the Drosophila life-cycle from fertilization to hatching. FBC:DOS Embryonic stage 1-3. pre-blastoderm FlyBase_development_CV FBdv:00005290 Temporal ordering number - 30. pre-blastoderm stage Embryonic stage 1-3. FBC:DOS 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). FlyBase_development_CV FBdv:00005291 Temporal ordering number - 40. embryonic stage 1 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). FlyBase:FBrf0064779 FlyBase:FBrf0089570 The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005292 Temporal ordering number - 50. embryonic cycle 1 The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 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). FlyBase_development_CV FBdv:00005293 Temporal ordering number - 70. embryonic stage 2 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). FlyBase:FBrf0089570 The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005294 Temporal ordering number - 60. embryonic cycle 2 The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005295 Temporal ordering number - 80. embryonic cycle 3 The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005296 Temporal ordering number - 90. embryonic cycle 4 The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005297 Temporal ordering number - 100. embryonic cycle 5 The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005298 Temporal ordering number - 110. embryonic cycle 6 The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005299 Temporal ordering number - 120. embryonic cycle 7 The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005300 Temporal ordering number - 130. embryonic cycle 8 The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 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). FlyBase_development_CV FBdv:00005301 Temporal ordering number - 140. embryonic stage 3 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). FlyBase:FBrf0089570 The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005302 Temporal ordering number - 150. embryonic cycle 9 The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The tenth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005303 Temporal ordering number - 180. embryonic cycle 10 The tenth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 Embryonic stages 4 and 5. blastoderm FlyBase_development_CV FBdv:00005304 Temporal ordering number - 160. blastoderm stage Embryonic stages 4 and 5. FBC:DOS FlyBase_development_CV FBdv:00005305 syncytial blastoderm stage true 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). syncytial blastoderm syncytial blastoderm stage FlyBase_development_CV FBdv:00005306 Temporal ordering number - 170. embryonic stage 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). FlyBase:FBrf0089570 The 11th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005307 Temporal ordering number - 185. embryonic cycle 11 The 11th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The 12th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005308 Temporal ordering number - 190. embryonic cycle 12 The 12th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 The 13th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase_development_CV FBdv:00005309 Temporal ordering number - 200. embryonic cycle 13 The 13th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo. FlyBase:FBrf0049535 FlyBase_development_CV FBdv:00005310 cellular blastoderm stage true 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). cellular blastoderm cellular blastoderm stage FlyBase_development_CV FBdv:00005311 Temporal ordering number - 210. embryonic stage 5 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). FlyBase:FBrf0089570 The 14th mitotic cell cycle of embryogenesis. This is the first round of nuclear division to occur in a cellularized embryo, so this is the first round of cell division. Embryonic cycle 14 mitosis is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains. first blastoderm mitosis FlyBase_development_CV FBdv:00005312 Temporal ordering number - 255. The asynchronous nature of cycle 14 divisions means that this is not very useful for annotating stage. If possible a standard embryonic stage should be used instead. embryonic cycle 14 The 14th mitotic cell cycle of embryogenesis. This is the first round of nuclear division to occur in a cellularized embryo, so this is the first round of cell division. Embryonic cycle 14 mitosis is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains. FlyBase:FBrf0049535 FlyBase:FBrf0089570 first blastoderm mitosis FlyBase:FBrf0089570 The interphase of embryonic cycle 14. This begins at the same time as cellularization and is of variable length depending on cell identity: embryonic cycle 14 M phase (14B) is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains. embryonic cycle 14 interphase FlyBase_development_CV FBdv:00005313 Temporal ordering number - 256. embryonic cycle 14A The interphase of embryonic cycle 14. This begins at the same time as cellularization and is of variable length depending on cell identity: embryonic cycle 14 M phase (14B) is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains. [FlyBase:FBrf0039741 embryonic cycle 14 interphase FBC:DOS The M-phase of embryonic cycle 14. This is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains. embryonic cycle 14 M-phase FlyBase_development_CV FBdv:00005314 Temporal ordering number - 257. Not to be confused with mitotic domain 14B, which is a domain of cells in the dorsal midline of the head that don't undergo a 14th division (Foe, 1989). The asynchronous nature of cycle 14 divisions means that this is not very useful for annotating stage. If possible a standard embryonic stage should be used instead. embryonic cycle 14B The M-phase of embryonic cycle 14. This is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains. FlyBase:FBrf0039741 embryonic cycle 14 M-phase FBC:DOS The 15th cell cycle of embryogenesis. Asynchronous. second blastoderm mitosis FlyBase_development_CV FBdv:00005315 Temporal ordering number - 285. The asynchronous nature of cycle 15 divisions means that this is not very useful for annotating stage. If possible a standard embryonic stage should be used instead. embryonic cycle 15 The 15th cell cycle of embryogenesis. Asynchronous. FlyBase:FBrf0089570 second blastoderm mitosis FlyBase:FBrf0089570 The 16th cell cycle division of embryogenesis. Asynchronous. third blastoderm mitosis FlyBase_development_CV FBdv:00005316 Temporal ordering number - 295. The asynchronous nature of cycle 16 divisions means that this is not very useful for annotating stage. If possible a standard embryonic stage should be used instead. embryonic cycle 16 The 16th cell cycle division of embryogenesis. Asynchronous. FlyBase:FBrf0089570 third blastoderm mitosis FlyBase:FBrf0089570 Stages during which gastrulation occurs. 6-8. gastrula FlyBase_development_CV FBdv:00005317 Temporal ordering number - 220. gastrula stage Stages during which gastrulation occurs. 6-8. FBC:DOS 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). FlyBase_development_CV FBdv:00005318 Temporal ordering number - 230. embryonic stage 6 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). FlyBase:FBrf0089570 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). FlyBase_development_CV FBdv:00005319 Temporal ordering number - 240. embryonic stage 7 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). FlyBase:FBrf0089570 FlyBase_development_CV FBdv:00005320 germ band stage true Stages during which the germ band is extended - 9-12. FlyBase_development_CV FBdv:00005321 Temporal ordering number - 260. extended germ band stage Stages during which the germ band is extended - 9-12. FBC:DOS 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). rapidly extending germ band stage FlyBase_development_CV FBdv:00005322 Temporal ordering number - 250. embryonic stage 8 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). FlyBase:FBrf0089570 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). FlyBase_development_CV FBdv:00005323 Temporal ordering number - 280. embryonic stage 9 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). FlyBase:FBrf0089570 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). FlyBase_development_CV FBdv:00005324 Temporal ordering number - 290. embryonic stage 10 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). FlyBase:FBrf0089570 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). FlyBase_development_CV FBdv:00005325 Temporal ordering number - 310. embryonic stage 11 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). FlyBase:FBrf0089570 FlyBase_development_CV FBdv:00005326 contracted germ band stage true 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). retracting germ band stage FlyBase_development_CV FBdv:00005327 Temporal ordering number - 320. embryonic stage 12 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). FlyBase:FBrf0089570 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). contracted germ band stage FlyBase_development_CV FBdv:00005328 Temporal ordering number - 340. embryonic stage 13 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). FlyBase:FBrf0089570 FBdv:00005330 FlyBase_development_CV FBdv:00005329 head involution stage true 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). head involution stage FlyBase_development_CV FBdv:00005330 Temporal ordering number - 350. embryonic stage 14 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). FlyBase:FBrf0089570 A collective term for stages 13-15. FlyBase_development_CV FBdv:00005331 Temporal ordering number - 330. dorsal closure stage A collective term for stages 13-15. FBC:DOS 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). FlyBase_development_CV FBdv:00005332 Temporal ordering number - 360. embryonic stage 15 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). FlyBase:FBrf0089570 Embryonic stages 16-17. FlyBase_development_CV FBdv:00005333 Temporal ordering number - 370. late embryonic stage Embryonic stages 16-17. FBC:DOS 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). FlyBase_development_CV FBdv:00005334 Temporal ordering number - 380. embryonic stage 16 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). FlyBase:FBrf0089570 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). FlyBase_development_CV FBdv:00005335 Temporal ordering number - 390. embryonic stage 17 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). FlyBase:FBrf0089570 The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation. FlyBase_development_CV FBdv:00005336 Temporal ordering number - 400. larval stage The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation. FBC:DOS 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). UBERON:8000000 L1 first instar larva FlyBase_development_CV FBdv:00005337 Temporal ordering number - 410. first instar larval stage 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). FlyBase:FBrf0007733 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). UBERON:8000001 L2 second instar larva FlyBase_development_CV FBdv:00005338 Temporal ordering number - 420. second instar larval stage 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). FlyBase:FBrf0007733 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). UBERON:8000002 L3 FlyBase_development_CV third instar larva FBdv:00005339 Temporal ordering number - 430. third instar larval stage 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). FlyBase:FBrf0007733 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.). david 2008-11-13T11:51:56Z FlyBase_development_CV FBdv:00005340 Temporal ordering number - 440. early third instar larval stage 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.). FlyBase:FBrf0049147 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. david 2008-11-13T11:55:46Z late third instar post-feeding larva FlyBase_development_CV FBdv:00005341 Temporal ordering number - 460. wandering third instar larval stage 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. FlyBase:FBrf0049147 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). FlyBase_development_CV FBdv:00005342 Temporal ordering number - 500. prepupal 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 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). pupal stage P1 puparium formation white puparium stage pupal stage P0 white prepupa FlyBase_development_CV FBdv:00005343 Temporal ordering number - 510. prepupal stage P1 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 puparium formation FlyBase:FBrf0036849 white puparium stage FlyBase:FBrf0036849 pupal stage P0 FlyBase:FBrf0036849 white prepupa FlyBase:FBrf0036849 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). brown puparium stage pupal stage P2 FlyBase_development_CV FBdv:00005344 Temporal ordering number - 520. prepupal stage P2 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 brown puparium stage FlyBase:FBrf0036849 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). bubble prepupa stage pupal stage P3 FlyBase_development_CV FBdv:00005345 Temporal ordering number - 530. prepupal stage P3 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 bubble prepupa stage FlyBase:FBrf0036849 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). cryptocephalic pupa pupal stage P4 FlyBase_development_CV FBdv:00005346 Temporal ordering number - 540. prepupal stage P4 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 cryptocephalic pupa FlyBase:FBrf0036849 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). buoyant stage pupal stage P4(i) FlyBase_development_CV FBdv:00005347 Temporal ordering number - 550. prepupal stage P4(i) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 buoyant stage FlyBase:FBrf0036849 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). moving bubble stage pupal stage P4(ii) FlyBase_development_CV FBdv:00005348 Temporal ordering number - 560. prepupal stage P4(ii) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 moving bubble stage FlyBase:FBrf0036849 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). phanerocephalic pupa FlyBase_development_CV FBdv:00005349 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 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 phanerocephalic pupa FlyBase:FBrf0036849 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). FlyBase_development_CV FBdv:00005350 Temporal ordering number - 580. pupal stage P5 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 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 migrating FlyBase_development_CV FBdv:00005351 Temporal ordering number - 590. pupal stage P5(i) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 Malpighian tubules migrating FlyBase:FBrf0036849 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). white Malpighian tubules stage FlyBase_development_CV FBdv:00005352 Temporal ordering number - 600. pupal stage P5(ii) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 white Malpighian tubules stage FlyBase:FBrf0036849 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). green Malpighian tubules stage FlyBase_development_CV FBdv:00005353 Temporal ordering number - 610. pupal stage P6 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 green Malpighian tubules stage FlyBase:FBrf0036849 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). yellow body stage FlyBase_development_CV FBdv:00005354 Temporal ordering number - 620. pupal stage P7 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 yellow body stage FlyBase:FBrf0036849 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). pupal stage P8 yellow-eyed stage FlyBase_development_CV FBdv:00005355 Temporal ordering number - 630. pharate adult stage P8 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 yellow-eyed stage FlyBase:FBrf0036849 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). amber-eyed stage pupal stage P9 FlyBase_development_CV FBdv:00005356 Temporal ordering number - 640. pharate adult stage P9 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 amber-eyed stage FlyBase:FBrf0036849 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). pupal stage P10 red-eye bald stage FlyBase_development_CV FBdv:00005357 Temporal ordering number - 650. pharate adult stage P10 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 red-eye bald stage FlyBase:FBrf0036849 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). pupal stage P11 FlyBase_development_CV FBdv:00005358 Temporal ordering number - 660. pharate adult stage P11 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 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). head bristles stage pupal stage P11(i) FlyBase_development_CV FBdv:00005359 Temporal ordering number - 670. pharate adult stage P11(i) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 head bristles stage FlyBase:FBrf0036849 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). pupal stage P11(ii) thoracic bristles stage FlyBase_development_CV FBdv:00005360 Temporal ordering number - 680. pharate adult stage P11(ii) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 thoracic bristles stage FlyBase:FBrf0036849 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). pupal stage P12 FlyBase_development_CV FBdv:00005361 Temporal ordering number - 690. pharate adult stage P12 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 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). pupal stage P12(i) wing tips grey stage FlyBase_development_CV FBdv:00005362 Temporal ordering number - 700. pharate adult stage P12(i) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 wing tips grey stage FlyBase:FBrf0036849 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). pupal stage P12(ii) wings grey stage FlyBase_development_CV FBdv:00005363 Temporal ordering number - 710. pharate adult stage P12(ii) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 wings grey stage FlyBase:FBrf0036849 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). pupal stage P13 wings black stage FlyBase_development_CV FBdv:00005364 Temporal ordering number - 720. pharate adult stage P13 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 wings black stage FlyBase:FBrf0036849 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). mature bristles stage pupal stage P14 FlyBase_development_CV FBdv:00005365 Temporal ordering number - 730. pharate adult stage P14 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 mature bristles stage FlyBase:FBrf0036849 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). pupal stage P15 FlyBase_development_CV FBdv:00005366 Temporal ordering number - 740. pharate adult stage P15 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 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). meconium stage pupal stage P15(i) FlyBase_development_CV FBdv:00005367 Temporal ordering number - 750. pharate adult stage P15(i) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 meconium stage FlyBase:FBrf0036849 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). eclosion stage pupal stage P15(ii) FlyBase_development_CV FBdv:00005368 Temporal ordering number - 760. pharate adult stage P15(ii) 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 eclosion stage FlyBase:FBrf0036849 The stage of the Drosophila life-cycle from eclosion to death. FlyBase_development_CV FBdv:00005369 Temporal ordering number - 770. adult stage The stage of the Drosophila life-cycle from eclosion to death. FBC:DOS 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. FBdv:00005373 FlyBase_development_CV adult stage I FBdv:00005370 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. adult stage A1 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. FlyBase:FBrf0049147 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. FBdv:00005374 FlyBase_development_CV adult stage II FBdv:00005371 Temporal ordering number - 790. adult stage A2 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. FlyBase:FBrf0049147 true true true FlyBase_development_CV FBdv:00005412 This should be considered as a type of cell rather than as a stage. Please use FBbt:00005412. gamete true 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). FlyBase_development_CV FBdv:00006011 Temporal ordering number - 625. pharate adult stage 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). FlyBase:FBrf0036849 FlyBase:FBrf0048355 FlyBase:FBrf0049147 Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C. FBdv:00005375 FlyBase_development_CV adult stage III FBdv:00006012 Temporal ordering number - 800. adult stage A3 Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C. FlyBase:FBrf0049147 david 2008-06-05T04:51:08Z GO:0007283 FlyBase_development_CV FBdv:00007000 Temporal ordering number - 20000. spermatogenesis The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion. david 2008-06-05T04:51:40Z metamorphosis FlyBase_development_CV pupal stage FBdv:00007001 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. P-stage The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion. FBC:DOS Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins and ends when the dorsal appendages begin to form. FlyBase_development_CV FBdv:00007002 Temporal ordering number - 10140. oogenesis stage S11a Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins and ends when the dorsal appendages begin to form. FlyBase:FBrf0043885 Oogenesis stage that begins when endochorion begins to form at the anterior pole, a process which includes the beginning of formation of the dorsal appendages. During this stage, the follicle cells secrete membranous vesicles that form irregular extracellular plaques. This stage ends when dying nurse cells form an anterior cap to the oocyte. FlyBase_development_CV FBdv:00007003 Temporal ordering number - 10150. oogenesis stage S11b Oogenesis stage that begins when endochorion begins to form at the anterior pole, a process which includes the beginning of formation of the dorsal appendages. During this stage, the follicle cells secrete membranous vesicles that form irregular extracellular plaques. This stage ends when dying nurse cells form an anterior cap to the oocyte. FlyBase:FBrf0043885 Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage. FlyBase_development_CV FBdv:00007004 Temporal ordering number - 470. third instar larval stage L1 Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage. FlyBase:FBrf0036849 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. spiracles everted larva FlyBase_development_CV white prepupa FBdv:00007005 Temporal ordering number - 480. third instar larval stage L2 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. FlyBase:FBrf0036849 spiracles everted larva FlyBase:FBrf0036849 white prepupa FlyBase:FBrf0036849 Oogenesis stage during which the number of nurse cell nuclei at the anterior of the oocyte reduce from 4 to zero. The oocyte chromosomes reach full metaphase I during this stage, at which point meiosis is arrested (until fertilization). david 2008-11-13T06:27:57Z FlyBase_development_CV FBdv:00007006 Temporal ordering number - 10250. oogenesis stage S13E Oogenesis stage during which the number of nurse cell nuclei at the anterior of the oocyte reduce from 4 to zero. The oocyte chromosomes reach full metaphase I during this stage, at which point meiosis is arrested (until fertilization). FlyBase:FBrf0029744 Third instar larva from the beginning of wandering to the beginning of puparium formation. david 2008-12-11T01:19:53Z FlyBase_development_CV FBdv:00007007 Temporal ordering number - 450. late third instar larval stage Third instar larva from the beginning of wandering to the beginning of puparium formation. FBC:DOS FlyBase_development_CV FBdv:00007008 occurrent true djs93 2009-10-01T05:56:42Z GO:0032502 FlyBase_development_CV FBdv:00007009 developmental process true 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. djs93 2009-10-01T05:57:41Z FlyBase_development_CV FBdv:00007011 embryonic cycle 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. FlyBase:FBrf0049535 FlyBase:FBrf0089570 A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion. djs93 2009-10-01T05:59:22Z life cycle stage FlyBase_development_CV FBdv:00007012 life stage A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion. FBC:DOS Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion. djs93 2010-09-29T12:25:36Z FlyBase_development_CV FBdv:00007013 age Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion. FBC:DOS Temporal subdivision of adulthood in days post-eclosion. djs93 2010-09-29T12:28:05Z FlyBase_development_CV FBdv:00007014 adult age in days Temporal subdivision of adulthood in days post-eclosion. FBC:DOS The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying). djs93 2011-04-26T11:57:15Z FlyBase_development_CV FBdv:00007015 Temporal ordering number - 391. Should not be used to stage embryos whose development is at temperatures other than 25'C. embryonic stage 17(i) The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying). FBC:DOS Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying). djs93 2011-04-26T12:00:15Z FlyBase_development_CV FBdv:00007016 Temporal ordering number - 392. Should not be used to stage embryos whose development is at temperatures other than 25'C. embryonic stage 17(ii) Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying). FBC:DOS Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying). djs93 2011-04-26T12:01:18Z FlyBase_development_CV FBdv:00007017 Temporal ordering number - 393. Should not be used to stage embryos whose development is at temperatures other than 25'C. embryonic stage 17(iii) Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying). FBC:DOS Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying). djs93 2011-04-26T12:03:14Z FlyBase_development_CV FBdv:00007018 Temporal ordering number - 394. Should not be used to stage embryos whose development is at temperatures other than 25'C. embryonic stage 17(iv) Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying). FBC:DOS The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut. FlyBase_development_CV FBdv:00007019 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). third instar - uncleared gut stage The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut. FlyBase:FBrf0076598 The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents. FlyBase_development_CV FBdv:00007020 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 partially cleared its gut contents. FlyBase:FBrf0076598 The substage of the wandering third instar larval stage when the larva has cleared its gut contents. FlyBase_development_CV FBdv:00007021 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. third instar - cleared gut stage The substage of the wandering third instar larval stage when the larva has cleared its gut contents. FlyBase:FBrf0076598 The interphase (GO:0051325) of an embryonic cycle. FlyBase_development_CV FBdv:00007022 embryonic cycle interphase The interphase (GO:0051325) of an embryonic cycle. FBC:DOS The M-phase (GO:0000279) of an embryonic cycle. FlyBase_development_CV FBdv:00007023 embryonic cycle M-phase The M-phase (GO:0000279) of an embryonic cycle. FBC:DOS GO:0008150 FlyBase_development_CV FBdv:00007024 biological process The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3). djs93 2013-01-08T20:06:59Z FlyBase_development_CV FBdv:00007025 Temporal ordering number - 782. immature adult stage The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3). FBC:DOS Life stage from the end of adult stage A3, when tanning is complete, to death. djs93 2013-01-10T13:03:54Z FlyBase_development_CV FBdv:00007026 mature adult stage Life stage from the end of adult stage A3, when tanning is complete, to death. FBC:DOS The day of eclosion. FlyBase_development_CV FBdv:00007075 Temporal ordering number - 780. day 0 of adulthood The day of eclosion. FBC:DOS 1st day after eclosion. FlyBase_development_CV FBdv:00007076 Temporal ordering number - 810. day 1 of adulthood 1st day after eclosion. FBC:DOS 2nd day after eclosion. FlyBase_development_CV FBdv:00007077 Temporal ordering number - 820. day 2 of adulthood 2nd day after eclosion. FBC:DOS 3rd day after eclosion. FlyBase_development_CV FBdv:00007078 Temporal ordering number - 830. day 3 of adulthood 3rd day after eclosion. FBC:DOS 4th day after eclosion. FlyBase_development_CV FBdv:00007079 Temporal ordering number - 840. day 4 of adulthood 4th day after eclosion. FBC:DOS 5th day after eclosion. FlyBase_development_CV FBdv:00007080 Temporal ordering number - 850. day 5 of adulthood 5th day after eclosion. FBC:DOS 6th day after eclosion. FlyBase_development_CV FBdv:00007081 Temporal ordering number - 860. day 6 of adulthood 6th day after eclosion. FBC:DOS 7th day after eclosion. FlyBase_development_CV FBdv:00007082 Temporal ordering number - 870. day 7 of adulthood 7th day after eclosion. FBC:DOS 8th day after eclosion. FlyBase_development_CV FBdv:00007083 Temporal ordering number - 880. day 8 of adulthood 8th day after eclosion. FBC:DOS 9th day after eclosion. FlyBase_development_CV FBdv:00007084 Temporal ordering number - 890. day 9 of adulthood 9th day after eclosion. FBC:DOS 10th day after eclosion. FlyBase_development_CV FBdv:00007085 Temporal ordering number - 900. day 10 of adulthood 10th day after eclosion. FBC:DOS 11th day after eclosion. FlyBase_development_CV FBdv:00007086 Temporal ordering number - 910. day 11 of adulthood 11th day after eclosion. FBC:DOS 12th day after eclosion. FlyBase_development_CV FBdv:00007087 Temporal ordering number - 920. day 12 of adulthood 12th day after eclosion. FBC:DOS 13th day after eclosion. FlyBase_development_CV FBdv:00007088 Temporal ordering number - 930. day 13 of adulthood 13th day after eclosion. FBC:DOS 14th day after eclosion. FlyBase_development_CV FBdv:00007089 Temporal ordering number - 940. day 14 of adulthood 14th day after eclosion. FBC:DOS 15th day after eclosion. FlyBase_development_CV FBdv:00007090 Temporal ordering number - 950. day 15 of adulthood 15th day after eclosion. FBC:DOS 16th day after eclosion. FlyBase_development_CV FBdv:00007091 Temporal ordering number - 960. day 16 of adulthood 16th day after eclosion. FBC:DOS 17th day after eclosion. FlyBase_development_CV FBdv:00007092 Temporal ordering number - 970. day 17 of adulthood 17th day after eclosion. FBC:DOS 18th day after eclosion. FlyBase_development_CV FBdv:00007093 Temporal ordering number - 980. day 18 of adulthood 18th day after eclosion. FBC:DOS 19th day after eclosion. FlyBase_development_CV FBdv:00007094 Temporal ordering number - 990. day 19 of adulthood 19th day after eclosion. FBC:DOS 20th day after eclosion. FlyBase_development_CV FBdv:00007095 Temporal ordering number - 1000. day 20 of adulthood 20th day after eclosion. FBC:DOS 21st day after eclosion. FlyBase_development_CV FBdv:00007096 Temporal ordering number - 1010. day 21 of adulthood 21st day after eclosion. FBC:DOS 22nd day after eclosion. FlyBase_development_CV FBdv:00007097 Temporal ordering number - 1020. day 22 of adulthood 22nd day after eclosion. FBC:DOS 23rd day after eclosion. FlyBase_development_CV FBdv:00007098 Temporal ordering number - 1030. day 23 of adulthood 23rd day after eclosion. FBC:DOS 24th day after eclosion. FlyBase_development_CV FBdv:00007099 Temporal ordering number - 1040. day 24 of adulthood 24th day after eclosion. FBC:DOS 25th day after eclosion. FlyBase_development_CV FBdv:00007100 Temporal ordering number - 1050. day 25 of adulthood 25th day after eclosion. FBC:DOS 26th day after eclosion. FlyBase_development_CV FBdv:00007101 Temporal ordering number - 1060. day 26 of adulthood 26th day after eclosion. FBC:DOS 27th day after eclosion. FlyBase_development_CV FBdv:00007102 Temporal ordering number - 1070. day 27 of adulthood 27th day after eclosion. FBC:DOS 28th day after eclosion. FlyBase_development_CV FBdv:00007103 Temporal ordering number - 1080. day 28 of adulthood 28th day after eclosion. FBC:DOS 29th day after eclosion. FlyBase_development_CV FBdv:00007104 Temporal ordering number - 1090. day 29 of adulthood 29th day after eclosion. FBC:DOS 30th day after eclosion. FlyBase_development_CV FBdv:00007105 Temporal ordering number - 1100. day 30 of adulthood 30th day after eclosion. FBC:DOS 31st day after eclosion. FlyBase_development_CV FBdv:00007106 Temporal ordering number - 1110. day 31 of adulthood 31st day after eclosion. FBC:DOS 32nd day after eclosion. FlyBase_development_CV FBdv:00007107 Temporal ordering number - 1120. day 32 of adulthood 32nd day after eclosion. FBC:DOS 33rd day after eclosion. FlyBase_development_CV FBdv:00007108 Temporal ordering number - 1130. day 33 of adulthood 33rd day after eclosion. FBC:DOS 34th day after eclosion. FlyBase_development_CV FBdv:00007109 Temporal ordering number - 1140. day 34 of adulthood 34th day after eclosion. FBC:DOS 35th day after eclosion. FlyBase_development_CV FBdv:00007110 Temporal ordering number - 1150. day 35 of adulthood 35th day after eclosion. FBC:DOS 36th day after eclosion. FlyBase_development_CV FBdv:00007111 Temporal ordering number - 1160. day 36 of adulthood 36th day after eclosion. FBC:DOS 37th day after eclosion. FlyBase_development_CV FBdv:00007112 Temporal ordering number - 1170. day 37 of adulthood 37th day after eclosion. FBC:DOS 38th day after eclosion. FlyBase_development_CV FBdv:00007113 Temporal ordering number - 1180. day 38 of adulthood 38th day after eclosion. FBC:DOS 39th day after eclosion. FlyBase_development_CV FBdv:00007114 Temporal ordering number - 1190. day 39 of adulthood 39th day after eclosion. FBC:DOS 40th day after eclosion. FlyBase_development_CV FBdv:00007115 Temporal ordering number - 1200. day 40 of adulthood 40th day after eclosion. FBC:DOS 41st day after eclosion. FlyBase_development_CV FBdv:00007116 Temporal ordering number - 1210. day 41 of adulthood 41st day after eclosion. FBC:DOS 42nd day after eclosion. FlyBase_development_CV FBdv:00007117 Temporal ordering number - 1220. day 42 of adulthood 42nd day after eclosion. FBC:DOS 43rd day after eclosion. FlyBase_development_CV FBdv:00007118 Temporal ordering number - 1230. day 43 of adulthood 43rd day after eclosion. FBC:DOS 44th day after eclosion. FlyBase_development_CV FBdv:00007119 Temporal ordering number - 1240. day 44 of adulthood 44th day after eclosion. FBC:DOS 45th day after eclosion. FlyBase_development_CV FBdv:00007120 Temporal ordering number - 1250. day 45 of adulthood 45th day after eclosion. FBC:DOS 46th day after eclosion. FlyBase_development_CV FBdv:00007121 Temporal ordering number - 1260. day 46 of adulthood 46th day after eclosion. FBC:DOS 47th day after eclosion. FlyBase_development_CV FBdv:00007122 Temporal ordering number - 1270. day 47 of adulthood 47th day after eclosion. FBC:DOS 48th day after eclosion. FlyBase_development_CV FBdv:00007123 Temporal ordering number - 1280. day 48 of adulthood 48th day after eclosion. FBC:DOS 49th day after eclosion. FlyBase_development_CV FBdv:00007124 Temporal ordering number - 1290. day 49 of adulthood 49th day after eclosion. FBC:DOS 50th day after eclosion. FlyBase_development_CV FBdv:00007125 Temporal ordering number - 1300. day 50 of adulthood 50th day after eclosion. FBC:DOS 51st day after eclosion. FlyBase_development_CV FBdv:00007126 Temporal ordering number - 1310. day 51 of adulthood 51st day after eclosion. FBC:DOS 52nd day after eclosion. FlyBase_development_CV FBdv:00007127 Temporal ordering number - 1320. day 52 of adulthood 52nd day after eclosion. FBC:DOS 53rd day after eclosion. FlyBase_development_CV FBdv:00007128 Temporal ordering number - 1330. day 53 of adulthood 53rd day after eclosion. FBC:DOS 54th day after eclosion. FlyBase_development_CV FBdv:00007129 Temporal ordering number - 1340. day 54 of adulthood 54th day after eclosion. FBC:DOS 55th day after eclosion. FlyBase_development_CV FBdv:00007130 Temporal ordering number - 1350. day 55 of adulthood 55th day after eclosion. FBC:DOS 56th day after eclosion. FlyBase_development_CV FBdv:00007131 Temporal ordering number - 1360. day 56 of adulthood 56th day after eclosion. FBC:DOS 57th day after eclosion. FlyBase_development_CV FBdv:00007132 Temporal ordering number - 1370. day 57 of adulthood 57th day after eclosion. FBC:DOS 58th day after eclosion. FlyBase_development_CV FBdv:00007133 Temporal ordering number - 1380. day 58 of adulthood 58th day after eclosion. FBC:DOS 59th day after eclosion. FlyBase_development_CV FBdv:00007134 Temporal ordering number - 1390. day 59 of adulthood 59th day after eclosion. FBC:DOS 60th day after eclosion. FlyBase_development_CV FBdv:00007135 Temporal ordering number - 1400. day 60 of adulthood 60th day after eclosion. FBC:DOS A collective term for stages 9 and 10. FlyBase_development_CV FBdv:00014201 Temporal ordering number - 270. early extended germ band stage A collective term for stages 9 and 10. FBC:DOS true A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. M phase of mitotic cell cycle M-phase of mitotic cell cycle biological_process GO:0000087 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. GOC:mtg_cell_cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 Wikipedia:Mitosis biological_process mitosis GO:0000278 Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. Wikipedia:M_phase M-phase biological_process GO:0000279 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. GOC:mtg_cell_cycle The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis GO:0000280 nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah molecular process molecular_function catalytic activity A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. GOC:go_curators GOC:mtg_cell_cycle The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). https://github.com/geneontology/go-ontology/issues/21234 biological_process GO:0007275 Note that this term was 'developmental process'. multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:dph GOC:ems GOC:isa_complete GOC:tb A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis embryonal development biological_process GO:0009790 embryo development The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GOC:go_curators GOC:isa_complete GOC:mtg_sensu Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0022403 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). cell cycle phase One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:mtg_cell_cycle Any biological process, occurring at the level of a multicellular organism, pertinent to its function. jl 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. jl 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete A distinct period or stage in a biological process or cycle. jl 2014-07-16T13:12:40Z biological_process GO:0044848 Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase. biological phase A distinct period or stage in a biological process or cycle. GOC:jl The eukaryotic cell cycle in which a cell is duplicated without changing ploidy, occurring in the embryo. biological_process GO:0045448 mitotic cell cycle, embryonic The eukaryotic cell cycle in which a cell is duplicated without changing ploidy, occurring in the embryo. GOC:go_curators The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission The creation of two or more organelles by division of one organelle. GOC:jid The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure biological_process GO:0048856 anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. resting phase Wikipedia:Interphase karyostasis biological_process GO:0051325 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). interphase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. GOC:mtg_cell_cycle The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. interphase of mitotic cell cycle biological_process GO:0051329 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic interphase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. GOC:mtg_cell_cycle A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. mah 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0098763 This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic cell cycle phase One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:dos A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T14:44:23Z mitosis biological_process GO:0140014 mitotic nuclear division A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. ISBN:0198547684 A process that is part of the mitotic cell cycle. jl 2014-05-22T14:22:34Z biological_process GO:1903047 mitotic cell cycle process A process that is part of the mitotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 quality (PATO) quality 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X