meiotic cell cycle problem

[gocentral]

I'm trying to get some data from the cell cycel portion of the graph for Jurg.

i just spotted this, which looks like an anomaly...

meiotic cell cycle is part of cell cycle meiosis is part of cell cycle (indirectly)

BUT the definition of meiosis is

Definition Progression through meiosis, the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiosis occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations.

so it seems to be broader than 'meiotic cell cycle'

it seems as though it should be

meiosis --meiotic cell cycle

or that these 2 terms represent the same process.....

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/5215":https://sourceforge.net/p/geneontology/ontology-requests/5215

[gocentral]

• summary: cell cycle problem --> meiotic cell cycle problem

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423 Originator: NO

> meiotic cell cycle is part of cell cycle

no, meiotic cell cycle is is_a cell cycle, which looks ok

Meiosis is defined as a type of division, whereas meiotic cell cycle is defined as an entire cell cycle, including interphase. I think the only thing that needs changing is the wording of the meiosis def, to make it clearer that it refers to the M phases.

m

Original comment by: mah11

[gocentral]

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meiosis def reworded ... with luck, it won't cause a ruckus ... m

p.s. 'meiosis' is the only child of 'M phase of meiotic cell cycle', and I think the only reason we haven't merged them is the screaming that would ensue.

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori
• labels: --> Other term-related request
• milestone: --> 224410
• status: open --> closed-works-for-me

Original comment by: mah11

[gocentral]

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OK I still have a few 'issues' here

Look at the children of meiosis, they include GO:0030989 : horsetail nuclear movement (this might be ok) GO:0045141 : meiotic telomere clustering (this might be ok) GO:0048236 : plant-type spore development and even stuff under female meiosis like: polar body extrusion after meiotic division and spindle assembly involved in female meiosis

its TVP city under here....these things don't all appear to be M-phase specific.

This happens because people are thinking of differnt processes i)the broader 'meiotic development' and ii) the narrower 'meitoic division', but occasionally use the same term for annotatin (meiosis) (we don't currently have a term for 'meiotic development' there is a SF item about this somewhere....I know I have used the current meiosis term for 'meiotic development' and I need to revisit these and fix them)

I still think, if 'meiosis' and 'M phase of meiotic cell cycle' are equivalent here they should be merged and called "M phase of meiotic cell cycle" if this is what it means, if this is what we would do in any other situation.

wfh today btw,

Original comment by: ValWood

[gocentral]

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> Look at the children of meiosis ... it's TPV city

OK, we can move terms up to be directly under 'meiotic cell cycle' if they don't occur in M phase. Which ones?

> This happens because people are thinking of differnt processes > i) the broader 'meiotic development'

Is 'meiotic development' different from progressing through a meiotic cell cycle?

> I still think, if > 'meiosis' and 'M phase of meiotic cell cycle' > are equivalent here they should be merged

and I would love to be able to do that, but for this item I just went back and read parts of the old cell cycle mail threads ... I just don't have the energy to face the storm that would break out if we did that merge. <sigh> i'm gettin' old ...

Original comment by: mah11

[gocentral]

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I think of 'meiotic development as being the broader process of 'development of a haploid cell, so for yeast this would include conjugation, ascospore formation and its parts, so yes thay are different.

meiotic development would include "the formation of gametes", which would make sense as the current def says it occurs 'during the formation of gametes"

I thought we got older and wiser, but I'm happy for you to leave this (can always get merged eventually when it no longer makes sense to have the 2 terms), I'm not sure which tems need moving in addition to the ones I spotted, I would need to go through them all and I haven't yet worked out how to get a list of all child terms without going to each node individually (see help desk question yesterday for something else).

I think though that some of these (plant type spore development) would go under the proposed development term (if like in yeast the spore development occurs after the 2 meiotic divisions which I imagine it must, but you never know.....

Original comment by: ValWood

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> I think of 'meiotic development as being the broader process of > 'development of a haploid cell

I might have to leave that to the developmentally clued among us ...

> haven't yet worked out how to get a list of all child terms > without going to each node individually

For just the terms, maybe I can do a query in OBO-Edit. Which ones exactly? Descendants of 'meiosis'?

m

Original comment by: mah11

[gocentral]

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yep, If you send me a list, I'll look through and post the ones I don't think belong back here.

my other SF item. 1831804 yeast meiotic development was also to do with this.

Original comment by: ValWood

[gocentral]

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OK, here ya go ... all descendants, not just direct children (dead easy in OBO-Edit)

GO:0000705 achiasmate meiosis I GO:0009971 anastral spindle assembly involved in male meiosis GO:0051455 attachment of spindle microtubules to kinetochore during meiosis I GO:0051456 attachment of spindle microtubules to kinetochore during meiosis II GO:0051316 attachment of spindle microtubules to kinetochore during meiotic chromosome segregation GO:0051317 attachment of spindle microtubules to meiotic chromosome GO:0032121 attachment of telomeres to spindle pole body GO:0051026 chiasma formation GO:0000241 diakinesis GO:0000240 diplotene GO:0032837 distributive segregation GO:0042139 early meiotic recombination nodule assembly GO:0034089 establishment of meiotic sister chromatid cohesion GO:0007143 female meiosis GO:0016321 female meiosis chromosome segregation GO:0051309 female meiosis chromosome separation GO:0007144 female meiosis I GO:0007147 female meiosis II GO:0007066 female meiosis sister chromatid cohesion GO:0016345 female meiotic chromosome movement towards spindle pole GO:0051758 homologous chromosome movement towards spindle pole during meiosis I GO:0031619 homologous chromosome orientation during meiosis GO:0045143 homologous chromosome segregation GO:0030989 horsetail nuclear movement GO:0042140 late meiotic recombination nodule assembly GO:0051878 lateral element assembly GO:0000237 leptotene GO:0030999 linear element formation GO:0034090 maintenance of meiotic sister chromatid cohesion GO:0007140 male meiosis GO:0007060 male meiosis chromosome segregation GO:0051308 male meiosis chromosome separation GO:0007141 male meiosis I GO:0007142 male meiosis II GO:0007065 male meiosis sister chromatid cohesion GO:0016346 male meiotic chromosome movement towards spindle pole GO:0009554 megasporogenesis GO:0007127 meiosis I GO:0051079 meiosis I nuclear envelope disassembly GO:0051334 meiosis I nuclear envelope reassembly GO:0007135 meiosis II GO:0051080 meiosis II nuclear envelope disassembly GO:0051335 meiosis II nuclear envelope reassembly GO:0007133 meiotic anaphase I GO:0007138 meiotic anaphase II GO:0051178 meiotic chromosome decondensation GO:0016344 meiotic chromosome movement towards spindle pole GO:0045132 meiotic chromosome segregation GO:0051307 meiotic chromosome separation GO:0042138 meiotic DNA double-strand break formation GO:0000706 meiotic DNA double-strand break processing GO:0000707 meiotic DNA recombinase assembly GO:0000711 meiotic DNA repair synthesis GO:0008315 meiotic G2/MI transition GO:0006311 meiotic gene conversion GO:0000713 meiotic heteroduplex formation GO:0000709 meiotic joint molecule formation GO:0007132 meiotic metaphase I GO:0043060 meiotic metaphase I plate congression GO:0007137 meiotic metaphase II GO:0043061 meiotic metaphase II plate congression GO:0051311 meiotic metaphase plate congression GO:0000710 meiotic mismatch repair GO:0007128 meiotic prophase I GO:0007136 meiotic prophase II GO:0007131 meiotic recombination GO:0051598 meiotic recombination checkpoint GO:0007146 meiotic recombination nodule assembly GO:0051755 meiotic sister chromatid arm separation GO:0051756 meiotic sister chromatid centromere separation GO:0051177 meiotic sister chromatid cohesion GO:0051760 meiotic sister chromatid cohesion, arms GO:0051754 meiotic sister chromatid cohesion, centromeric GO:0045144 meiotic sister chromatid segregation GO:0051757 meiotic sister chromatid separation GO:0000714 meiotic strand displacement GO:0000708 meiotic strand invasion GO:0045141 meiotic telomere clustering GO:0007134 meiotic telophase I GO:0007139 meiotic telophase II GO:0009556 microsporogenesis GO:0034095 negative regulation of maintenance of meiotic sister chromatid cohesion GO:0045835 negative regulation of meiosis GO:0045128 negative regulation of meiotic recombination GO:0000239 pachytene GO:0048236 plant-type spore development GO:0040038 polar body extrusion after meiotic divisions GO:0034096 positive regulation of maintenance of meiotic sister chromatid cohesion GO:0045836 positive regulation of meiosis GO:0034094 regulation of maintenance of meiotic sister chromatid cohesion GO:0040020 regulation of meiosis GO:0010520 regulation of meiotic recombination GO:0000712 resolution of meiotic joint molecules as recombinants GO:0051759 sister chromosome movement towards spindle pole during meiosis II GO:0007056 spindle assembly involved in female meiosis GO:0007057 spindle assembly involved in female meiosis I GO:0007058 spindle assembly involved in female meiosis II GO:0007053 spindle assembly involved in male meiosis GO:0007054 spindle assembly involved in male meiosis I GO:0007055 spindle assembly involved male meiosis II GO:0007129 synapsis GO:0007130 synaptonemal complex assembly GO:0000238 zygotene

Original comment by: mah11

[gocentral]

• status: closed-works-for-me --> open

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865 Originator: YES

These appear to refer to a broader process of meiotic or haploid development GO:0009554 megasporogenesis GO:0009556 microsporogenesis GO:0048236 plant-type spore development GO:0040038 polar body extrusion after meiotic divisions

Not sure about these, maybe they should move up from meiosis and just have meiotic cell cycle: GO:0045141 meiotic telomere clustering GO:0032121 attachment of telomeres to spindle pole body

GO:0007143 female meiosis (this isn’t clear as is it is defined as "mieosis in the female germline", but it has children like... GO:0007056 spindle assembly involved in female meiosis, Which is not M-phase specific (is it?) ditto GO:0007140 male meiosis GO:0007053 spindle assembly involved in male meiosis GO:0009971 anastral spindle assembly involved in male meiosis

not sure if this is an M-phase specific process? probably not... GO:0051178 meiotic chromosome decondensation

Original comment by: ValWood

[gocentral]

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moved GO:0048236 up, which also takes care of GO:0009554 and GO:0009556

I think GO:0040038 is OK, even though the name says 'after', because polar bodies form during the meiotic divisions. Spindle assembly is M-phase-specific. Chromosome decondensation normally occurs during telophase.

Original comment by: mah11

[gocentral]

• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11