rearrange oogenesis (sensu Insecta) child terms

[gocentral]

Several GO terms (below) are children of oogenesis (sensu Insecta) [9993], but these terms each have other parental trees that are not insect-specific. Curation of non-insect proteins to these terms is a true path violation, even though it looks legitimate, if a curator is viewing the non-insect parental trees for these terms. In most of these cases the insect process is distinct and fundamentally different from that in other organisms, so an insect-specific branch may be justified, but the definitions and 'sensu' qualifiers are not currently in place. One suggestion is that these terms be defined, with 'sensu Insecta' added, and then similar terms be developed for nemotodes (oogenesis (sensu Nematoda)), mammals (oogenesis (sensu Mammalia)) and other organisms.
Alternatively, we suggest that 'sensu Insecta' be removed, so that child terms are more species-general. Terms: oocyte axis determination 7309 oocyte dorsal/ventral axis determination 7310 oocyte cell fate determination 7294 oocyte nucleus migration 7312 polarization of the oocyte microtubule cytoskeleton 8103 organization of the oocyte microtubule cytoskeleton 16325 pole plasm assembly 7315 tl receptor signaling pathway 8063

Reported by: reneewhite

Original Ticket: "geneontology/ontology-requests/883":https://sourceforge.net/p/geneontology/ontology-requests/883

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Hi Renee,

I had a go at defining some of these terms last week (assuming they were sensu Insecta; see the attachment in SF:753304)... if its decided to go for the sensu Insecta version. If not most can be modified appropriately!

Thanks,

Becky

Original comment by: beckyfoulger

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Given that Becky has done all that work providing definitions, and the implicit meaning of the child terms (because they're under 'oogenesis (sensu Insecta)', I'd vote to add 'sensu Insecta' to the existing terms and add new terms for generic and sensu Nematoda, sensu Mammalia, etc.

m

Original comment by: mah11

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I agree with Midori's solution. We should make new generic parents and make each of these terms insect specific.

Original comment by: ukemi

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Tl receptor signaling pathway ; GO:0008063 should be removed as a child of oocyte dorsal/ventral axis determination ; GO:0007310. Toll signaling is involved in processes other than oogenesis in Drosophila anyway.

This should solve the TPV for this term.

Thanks, Becky

Original comment by: beckyfoulger

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Another term to add to this list is: cytoskeletal dependent cytoplasmic transport [19749]. It is insect-specific in the current ontology (under oogenesis (sensu Insecta)), and it would be nice to have a non-insect-specfic version of the term.

Original comment by: reneewhite

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OK, here's what I've done so far:

- added 'sensu Insecta' to a slew of terms under oogenesis (sensu Insecta) (9993): 7293-7295, 7297-7300, 7304, 7305, 8069-8071, 16350

- removed 8063 from under 7310 as Becky recommended

- moved 7308 up one level (directly under oogenesis 7292 instead of under 9993) because it was already defined as not insect specific

- added new generic terms: GO:0030703 eggshell formation GO:0030704 vitelline membrane formation GO:0030705 cytoskeleton-dependent intracellular transport

and rearranged relationships to accompany the new terms

- These terms were already not under 9993, so both wording and placement were non-insect-specific (no change required): 7309, 7310, 7312, 7315, 8103, 16325

- I have not yet added any new taxon-specific terms; we'll add them as and when needed, so please request specific ones.

Original comment by: mah11

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• assigned_to: nobody --> gomidori

Original comment by: mah11

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• assigned_to: gomidori --> jenclark

Original comment by: jenclark

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Hi Renee,

Midori has fixed the true path violations in the sensu Insecta terms. I'm now having a look at fixing up Mammalia, Nematoda etc. terms as you suggest. I was wondering if you can tell me if there are any specific Mammalia or Nematoda etc. terms that you need? It would be quite difficult to map out this whole area without knowing which terms are likely to be required. Also there is little sense in duplicating the sensu Insecta terms with a different sensu name, unless there has been shown to be some specific difference in the process involved.

Any specific term requests wuld be gratefully received.

Thanks,

Jen

Original comment by: jenclark

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I have written to the list to ask for specific term requests, so I'll not do anything until people get back to me.

Jen

Original comment by: jenclark

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Hi Jen and Midori- Thanks for all of the extensive rearrangements. We are happy with the changes - all of the terms that we would like to use are now in non-insect specific branches, or have generic parents. So there are no specific term requests at this time. We'll post any if they arise. Renee

Original comment by: reneewhite

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David Hill has contributed some sensu Mammalia terms that are needed so I'll add those in as well:

Here is what I have come up with for oogenesis in mammals. The basic stages are at the top and the details from things we already have are at the bottom. I don't know what to do about meiosis yet. I don't want to have to make a special mammalian oogenesis, but the part of issue and the true path rears its ugly head..

Oogenesis (sensu mammalia); GO:new <oogonium stage; GO:new; synonym:stage 1 <primary oocyte stage; GO:new; synonym:stage 2 <primary follicle stage; GO:new; synonym:stage 3 <double layer follicle stage; GO:new; synonym:stage 4 <multi-layer follicle stage; GO:new; synonym:stage 5 <scattered antral spaces stage; GO:new; synonym:stage 6 <distinct antral spaces stage; GO:new; synonym:stage 7 <fused antrum stage; GO:new; synonym:stage 8 <mature follicle stage; GO:new; synonym:stage 9

All defs are from ISBN 0-19-854277-1

Oogonium:The primordial germ cell is hardly distinguishable from other cortical cells of the ovary.

Primary oocyte:The oocyte has a nucleus slightly larger than those of the adjacent cells and is surrounded by a layer of loose squamous epithelial cells.

Primary follicle:A single layer of cuboidal follicle cells surrounds the oocyte. The oocyte nucleus is large.

Double layer follicle: A double layer of distinct follicle cells surrounds the oocyte.

Multi-layer follicle: Many layers of follicle cells surround the oocyte. There is a yolk nucleus (Balbiani's Body) near the germinal vesicle.

Scattered antral spaces: Antral spaces begin to form in the follicle cells. Mitochondria form centers for yolk concentration.

Distinct antral spaces: The antral spaces become distinct and the first polar body forms.

Fused antrum: The antral spaces fuse to form a single antral space. The oocyte is suspended in the cumulus oophorous and the first polar body in the perivitelline space.

Mature follicle: The antrum is swollen with follicular fluid. The ovum is ready to erupt from the ovary and is arrested at metaphase of the second meiotic division.

oocyte growth [GO:0001555] or a mammalian form of it will have to be a part of oogenesis. primary ovarian follicle growth [GO:0001545] and preantral ovarian follicle growth [GO:0001546] will have to be moved as parts of the correct stages of oogenesis (stage3-4 and stage 5 respectively). ovarian follicle antrum/follicular fluid formation [GO:0001548] will become a part of stages 6,7,8. ovarian cumulus expansion [GO:0001550] and ovarian cumulus cell differentiation [GO:0001549] will become parts of stage 8.

Original comment by: jenclark

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I have added these: oogenesis ; GO:0007292 --%oogenesis (sensu Mammalia); GO:new GO:0048157 ----<oogonium stage oogenesis; GO:new; synonym:mammalian oogenesis stage 1 GO:0048158 ----<primary oocyte stage oogenesis ; GO:new; synonym:mammalian oogenesis stage 2 GO:0048159 ----<primary follicle stage oogenesis; GO:new; synonym:mammalian oogenesis stage 3 GO:0048160 ----<double layer follicle stage oogenesis; GO:new; synonym:mammalian oogenesis stage 4 GO:0048161 ----<multi-layer follicle stage oogenesis; GO:new; synonym:mammalian oogenesis stage 5 GO:0048162 ----<scattered antral spaces stage oogenesis; GO:new; synonym:mammalian oogenesis stage 6 GO:0048163 ----<distinct antral spaces stage oogenesis; GO:new; synonym:mammalian oogenesis stage 7 GO:0048164 ----<fused antrum stage oogenesis; GO:new; synonym:mammalian oogenesis stage 8 GO:0048165 ----<mature follicle stage oogenesis; GO:new; synonym:mammalian oogenesis stage 9 GO:0048166

All defs are from ISBN 0198542771

oogenesis (sensu Mammalia) def: The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell, as seen in mammals.

oogonium stage oogenesis:The stage in mammalian oogenesis when the primordial germ cell is hardly distinguishable from other cortical cells of the ovary.

primary oocyte stage oogenesis:The stage in mammalian oogenesis when the oocyte has a nucleus slightly larger than those of the adjacent cells and is surrounded by a layer of loose squamous epithelial cells.

primary follicle stage oogenesis:The stage in mammalian oogenesis when a single layer of cuboidal follicle cells surrounds the oocyte. The oocyte nucleus is large.

double layer follicle stage oogenesis: The stage in mammalian oogenesis when a double layer of distinct follicle cells surrounds the oocyte.

multi-layer follicle stage oogenesis: The stage in mammalian oogenesis when many layers of follicle cells surround the oocyte. There is a yolk nucleus (Balbiani's Body) near the germinal vesicle.

scattered antral spaces stage oogenesis: The stage in mammalian oogenesis when antral spaces begin to form in the follicle cells. Mitochondria form centers for yolk concentration.

distinct antral spaces stage oogenesis: The stage in mammalian oogenesis when the antral spaces become distinct and the first polar body forms.

fused antrum stage oogenesis: The stage in mammalian oogenesis when the antral spaces fuse to form a single antral space. The oocyte is suspended in the cumulus oophorous and the first polar body in the perivitelline space.

mature follicle stage oogenesis: The stage in mammalian oogenesis when the antrum is swollen with follicular fluid. The ovum is ready to erupt from the ovary and is arrested at metaphase of the second meiotic division.

Original comment by: jenclark

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I still have the extra parentage for the mammalian terms to do but does any other species groups have more terms to contribute while I'm doing this?

Jen

Original comment by: jenclark

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I've done the extra parentage now so I'm going to close this item since it's getting pretty long now. If people would like more oogenesis terms then please do start a new SourceForge item.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-fixed

Original comment by: jenclark