hatching

[gocentral]

Flybase appears to be the only consortium group that has used the GO term "hatching" (GO:0035188). Well...fish hatch too! I would like to use that term, and the def does not preclude me from doing so. However, my gut feeling is that fly "hatching" and fish "hatching" and avian "hatching" may not be so similar. Are new terms needed as either children or sister terms to the current "hatching" term?

Any hatching experts out there?

-Doug

David Hill wrote: > It's true, blastocysts hatch from the zona. In sea urchins, blastula hatch from the fertilization envelope. This is an interesting case where I think these are all very different processes. I'm not sure if there would be utility in grouping them together. I'm not sure if any of the molecules involved in hatching are conserved in these different types. > > David > > > Alexander Diehl wrote: > >> Doug, >> >> "Hatching" even occurs in mice! >> >> Ask David for more details. >> >> -- Alex

Reported by: doughowe

Original Ticket: "geneontology/ontology-requests/3178":https://sourceforge.net/p/geneontology/ontology-requests/3178

[gocentral]

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Perhaps I should request a new term then "hatching (sensu Actinopterygii)to handle fish hatching?

There is already a term 'blastocyst hatching' (GO:0001835) that would be used for mammalian hatching.

-Doug

Original comment by: doughowe

[gocentral]

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How about this:

development (GO:0007275) ----[i] hatching (sensu Actinopterygii) (GO:NEW)

def: The emergence of an embryo from it's surrounding chorion as observed in the ray-finned fishes.

Original comment by: doughowe

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IF...IF...there is agreement that a new hatching term is useful/necessary....should the same logic apply to 'hatching behavior'? Zebrafish thrash briefly, and spring from their chorion in one violent motion...Drosophila apparently use mouth hooks to tear the chorion....Birds probably peck their way out I suppose...Turtles anyone??? And who knows how those sea urchins get out!

-Doug

-Doug

Original comment by: doughowe

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• assigned_to: nobody --> jenclark

Original comment by: jenclark

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I have written to the development list to get further comments.

Jen

Original comment by: jenclark

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Dicty people sometimes use hatching to refer to spore germination. Is that a general use of "hatching" in all organisms that form spores? If so, maybe we can have "hatching" as a synonym of spore germination.

But I would be happy to leave spores out of this!

Pascale

Original comment by: pgaudet

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hatching part_of development

def: The emergence of an embryo from a surrounding protective layer.

David

Original comment by: ukemi

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Hi David,

Will hatching part_of development

def: The emergence of an embryo from a surrounding protective layer.

be the sensu Mammalia term?

Jen

Original comment by: jenclark

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No, this will be the generic term. The sensu terms will go underneath. I think blastocyst hatching GO:0001835 will serve as the sensu mammalia term. Other folks should chime in, but it would make sense to also have an is_a path as:

extracellular matrix organization and biogenesis ; GO:0030198 --<extracellular matrix degradation ; GO:new ----%hatching

David

Original comment by: ukemi

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We'll need a sensu Amphibia term under GO:0035188 aswell, for the hatching of frog/toad etc embryos into tadpoles etc.

Original comment by: beckyfoulger

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extracellular matrix organization and biogenesis ; GO:0030198 --<extracellular matrix degradation ; GO:new ----%hatching

How does the above relate to avian hatching? They just plain old peck their way out as far as I know. There is no extracellular matrix degradation involved I don't think.

-Doug

Original comment by: doughowe

[gocentral]

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Good point! I'd like to come up with an is_a path. Could tehre be a mechanical degraedation of extracellular matrix? I don't know???????

Original comment by: ukemi

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Sorry about all the typos, I was still laughing as I typed that. It seems I failed to consider one of the most obvious examples of hatching!

Original comment by: ukemi

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Summary of what we have so far:

Hatching

Here's what we have so far:

[i]development ; GO:0007275 ---[i]hatching ; GO:0035188

hatching ; GO:0035188 def: The emergence of an organism from an egg.

[i]development ; GO:0007275 ---[i]embryonic development ; GO:0009790 ------[i]embryonic development (sensu Metazoa) ; GO:0009792 ---------[i]embryonic development (sensu Vertebrata) ; GO:0043009 ------------[i]embryonic development (sensu Mammalia) ; GO:0001701 ---------------[p]blastocyst development ; GO:0001824 ------------------[p]blastocyst hatching ; GO:0001835

blastocyst hatching ; GO:0001835 def: The hatching of the cellular blastocyst from the zona pellucida. (This is the mammalia term)

We also have suggestions:

[i]development (GO:0007275) ---[i]hatching (sensu Actinopterygii) (GO:NEW)

def: The emergence of an embryo from its surrounding chorion as observed in the ray-finned fishes.

Dicty spores:

Dicty people sometimes use hatching to refer to spore germination. Is that a general use of "hatching" in all organisms that form spores? If so, maybe we can have "hatching" as a synonym of spore germination.

generic hatching term:

[i]development ; GO:0007275 ----[i]hatching ; GO:new

hatching (sensu generic) def: The emergence of an embryo from a surrounding protective layer.

is_a path:

extracellular matrix organization and biogenesis ; GO:0030198 ---[p]mechanical matrix degradation ; GO:new ---{p]extracellular matrix degradation ; GO:new

[i]development ; GO:0007275 ---[i]hatching ; (generic) ------[i]hatching (sensu amphibia) ; GO:new

hatching (sensu amphibia) ; GO:new def: no def yet.

Hatching behavior

so far:

[i]development ; GO:0007275 ---[i]hatching ; GO:0035188 ------[p]hatching behavior ; GO:0035187 [i]response to stimulus ; GO:0050896
---[i]behavior ; GO:0007610
------[i]hatching behavior ; GO:0035187

suggestions:

Zebrafish thrash briefly, and spring from their chorion in one violent motion.

Drosophila apparently use mouth hooks to tear the chorion.

Birds probably peck their way out.

Original comment by: jenclark

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• priority: 5 --> 9

Original comment by: jenclark

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Hi Doug,

Did you need a specific term urgently here? It seems to me that we've got bogged down. If you need one specific term I can put that in and we can do the rest of th structure later.

jen

Original comment by: jenclark

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No urgency here. We are both swamped with brain development at the moment I suppose. I'm fine with just putting this one on hold for the time being, until it can again recieve proper attention.

-Doug

Original comment by: doughowe

[gocentral]

• priority: 9 --> 5

Original comment by: jenclark

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Logged In: YES user_id=436423 Originator: NO

Hi,

This item has been open for a long time. Please comment to let us know whether you would like it to remain assigned to you, or would prefer it to be reassigned. (You don't necessarily have to work on it immediately if you keep it; we just need to know whether it's still on your list.)

Thanks, Midori & David Ontology development group managers

Original comment by: mah11

[gocentral]

also see SF 2925595 (closed because I fixed the problem with 'eclosion', but could still be of interest for this)

https://sourceforge.net/tracker/?func=detail&aid=2925595&group\_id=36855&atid=440764

Original comment by: mah11

[gocentral]

• assigned_to: jenclark --> gomidori

Original comment by: jenclark

[gocentral]

Based on the comments that came in on the newer item, I've made a modest def edit for 'hatching' (GO:0035188), and added a new term as a parent for hatching and eclosion:

organism emergence from protective structure GO:0071684

Original comment by: mah11

[gocentral]

• milestone: --> Plant Ontology
• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• Group: Plant Ontology --> None

Original comment by: cooperl09