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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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make GO:0060468 | prevention of polyspermy more general #16329

Closed ValWood closed 3 years ago

ValWood commented 6 years ago

To describe the fertilization block in Nature. 2018 Aug;560(7718):397-400. Epub 2018 Aug 8. Gamete fusion triggers bipartite transcription factor assembly to block re-fertilization.

the authors selected the GO term: GO:0060468 | prevention of polyspermy

I wonder if we could generalise this term The negative regulation of fertilization process that takes place as part of egg activation, ensuring that only a single sperm fertilizes the egg.

i.e term name: negative regulation of re-fertilization?

The negative regulation of fertilization process after initial fertilization event that prevents the fusion of more than two gametes? Or something along those lines?

pgaudet commented 3 years ago

For info - regulation of fertilization is_a 'regulation of reproductive process'

Antonialock commented 3 years ago

are gene products that are involved in prevention of genome re-replication annotated to "negative regulation of DNA replication" (I can't think of specific example gps for this to check) @ValWood ?

if they are then I guess it could be a neg reg of reproductive process? (both "prevention of genome re-replication after the cell has done one round of S-phase" and "prevention of fusion with zygote" are both QC mechanisms so that the cell doesn't re-do a step it has already done in the flow of processes)

ValWood commented 3 years ago

wrong gene, but we usually annotatie as

negative regulation of mitotic DNA replication initiation

  | pop2   | cdc2 during mitotic G2 phase

i.e negative regulation outside of S-phase

Antonialock commented 3 years ago

till doesn't feel right in this context...maybe it's just me?

ensuring that a process progresses in the right order is not the same as negatively regulating the process?

ValWood commented 3 years ago

I don't know- but when I surveyed all of PomBase annotations to "regulation of blah" regulation falls into multiple classes and one of those I classed as "downstream regulation", negatively regulating the re-occurance of a process, or for example disassembling a structure after a process has occurred. So perhaps it is OK?

I think there is a lot of scope for defining different types of regulation more precisely (otherwise we will never know what we mean by regulation) but in the current system I don't think there is anything to prevent it being modelled in this way?

ValWood commented 3 years ago

I think it's fine because it's analogous to "prevention of polyspermy" and that has "negative regulation of fertilization parentage.

But it's a very good point that ideally, you need to know if this is negative regulation of the process beginning at all, or negative regulation of re-initiating a process.

Antonialock commented 3 years ago

ok thanks Val, that makes sense.

pgaudet commented 3 years ago

What's the action ?

ValWood commented 3 years ago

make

+id: GO:0140538 +name: negative regulation of conjugation with zygote

a regulation of fertilization

pgaudet commented 3 years ago

a regulation of fertilization

negative regulation of fertilization ?

Also part_of 'sexual reproduction' ?

sorry about the back and forth

pgaudet commented 3 years ago

'negative regulation of fertilization' is a already there - if you dont want part_of 'sexual reproduction' please close.

Wow - had you put 'quick fix' on that one ;) ???

ValWood commented 3 years ago

"Quick fix" label is the kiss of death....

I still can't use the term today, which means that something is still incorrect from the taxon?????

pgaudet commented 3 years ago

Yes - fertilization is a multiorganism process. We are going around in circles....

Antonialock commented 3 years ago

so can't sexual reproduction (or adecendant) be an instance where multi-organism process is ok for unicerllular organisms? (how can you sexually reproduce without involving more than one organism?)

ValWood commented 3 years ago

I think there is an issue with the logic somewhere. I still can't approve the session. I only took the session out of pom base out to add this new term, and now I can't get it back into PomBase. I feel really bad as it's an important recent Nature paper that a lot of people will look at and I'm sure the author will notice its absence soon....

https://curation.pombase.org/pombe/curs/46c89f342f117ca5

If it doesn't look like a fix is imminent I will remove the terms temporarily. What do you think? Does anyone know what the problem is? I don't?

@balhoff ?

ValWood commented 3 years ago

but multi organism process should. be OK for any species that does sexual reproduction. we use GO:0000747 conjugation with cellular fusion all the time with no problems?

mah11 commented 3 years ago

@balhoff explained in https://github.com/geneontology/go-ontology/issues/20362#issuecomment-726391379 that fertilization inherits never_in_taxon 'Schizosaccharomyces pombe' via an axiom in the Cell Ontology. (Note: QuickGO doesn't show these inherited taxon constraints.)

The text definition of GO:0140538 is less specific than the term name:

GO:0140538 ! negative regulation of conjugation with zygote def: "A process that prevents a zygote from fusing with additional cells." [PMID:30089908]

Having "conjugation" in the name also clashes with the link GO:0060468 ! prevention of polyspermy is_a GO:0140538, because sperm/egg fertilization is essentially never called conjugation.

Possible solutions:

ValWood commented 3 years ago

I am still unable to use +id: GO:0140538 +name: negative regulation of conjugation with zygote

Is it possible to implement one of the above solutions?

pgaudet commented 3 years ago

Sorry Val, Travis had been down.

I implemented the first suggestion:

GO:0140538 negative regulation of conjugation with zygote

GO:0060468 prevention of polyspermy

Should we still open a ticket for CL to remove 'capable of' some 'multicellular organismal reproductive process' from gamete (CL:0000300) ?

Thanks, Pascale

ValWood commented 3 years ago

Oh yes sorry I forgot about that, I wasn't sure there had been a final decision. Dying to get this one done!

pgaudet commented 3 years ago

OK done https://github.com/obophenotype/cell-ontology/issues/818

ValWood commented 3 years ago

ah right, is this about

Should we still open a ticket for CL to remove 'capable of' some 'multicellular organismal reproductive process' from gamete (CL:0000300) ?

@Antonialock said I also think that the paper uses some "unconventional yeast language" - probably to put it in context of the broader scientific audience. I don't think yeast researchers typically refer to vegetatative or shmooing cells as 'gametes'. Or 'fertilization'.

so I think we should have made

+id: GO:0140538 +name: negative regulation of conjugation with zygote

is_a

GO:0031138 negative regulation of conjugation with cellular fusion

not is_a GO:0060467 negative regulation of fertilization

ValWood commented 3 years ago

My fault sorry.

balhoff commented 3 years ago

I think we should have made

+id: GO:0140538 +name: negative regulation of conjugation with zygote

is_a

GO:0031138 negative regulation of conjugation with cellular fusion

not is_a GO:0060467 negative regulation of fertilization

Yes, I think this will remove the problem causing this to be excluded from pombe via --make-species-subset.

In general I think this ought be inferred rather than asserted.

ValWood commented 3 years ago

yay! I'm doing a little dance in my kitchen!