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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Taxon constraint: GO:0043045 post-fertilization epigenetic regulation of gene expression #26951

Closed ValWood closed 6 months ago

ValWood commented 7 months ago

Please provide as much information as you can:

GO:0043045 post-fertilization epigenetic regulation of gene expression

metazoa

pgaudet commented 7 months ago

There is a child term that represents a plant process, we cannot do 'only in metazoa'.

ValWood commented 7 months ago

OK will add "never in fungi"

cmungall commented 7 months ago

So many red flags with this term

It shouldn’t be necessary to make large numbers of never in fungi type annotation for classes that should have an existential restriction on embryonic development (we should go and make these non parsimonious assertions for practical reasons but it would be better to do this correctly)

I looked at the two pubmeds that supposedly support the creation of this term expecting to see an articulation of the concept but didn’t find any. If the concept doesn’t exist in the literature but was created by GO our provenance should reflect this.

The two child terms are fine, representing distinct processes in the zygote/endosperm

But “post fertilization “ seems like an odd grouping qualifier. Presumably part of the intent is to distinguish from imprinting which is pre fertilization. But is this a real concept a biologist would use? Is it a distinct program?

When we look at the definition there is also language about the state persisting over many cell divisions possibly into adulthood. This seems a bit vague and hard to use consistently. If the intent is in fact to use this only for changes in state initiated in embryogenesis and persisting to adulthood the name and definition could better reflect this.

If I was a user and I was interested in this concept I’d intersect all dna methylation genes, histone deac genes, with genes expressed during embryogenesis, then if I was interested in persistence of state further intersecting using genomic data. I believe this would get me a more accurate gene set than querying on the odd GO grouping.

On Mon, Feb 5, 2024 at 3:10 AM Val Wood @.***> wrote:

OK will add "never in fungi"

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pgaudet commented 7 months ago

Thanks for the comments @cmungall

In fact @colinlog and I just recently discussed merging GO:0043045 post-fertilization epigenetic regulation of gene expression with is child: GO:0044725 epigenetic programming in the zygotic pronuclei.

I am not sure to what extend you'd like to reduce this branch.

cmungall commented 7 months ago

In fact @colinlog and I just recently discussed merging GO:0043045 post-fertilization epigenetic regulation of gene expression with is child: GO:0044725 epigenetic programming in the zygotic pronuclei.

Does that definitely work with existing annotations? The text definition says "during embryonic development" which is very broad and I'm pretty sure some of the existing annotations describe things after the zygote.

Additionally we have a classic lopsided christmas tree structure:

"zygotic pronuclei" sounds metazoan but it's actually for animals or plants. However, plants annotate one level below. Animals annotate one level below if it's known if it's male or female.

pgaudet commented 6 months ago

@cmungall

To answer the 'easy' part of your comment above

If I was a user and I was interested in this concept I’d intersect all dna methylation genes, histone deac genes, with genes expressed during embryogenesis, then if I was interested in persistence of state further intersecting using genomic data. I believe this would get me a more accurate gene set than querying on the odd GO grouping.

This is what the grand-parent class epigenetic regulation of gene expression represents.

The challenge is to describe imprinting in plants and in animals.

pgaudet commented 6 months ago

After reviewing annotations, @colinlog and I have decided to change the label of

to 'epigenetic programming of gene expression' GO:0043045 ! post-fertilization epigenetic regulation of gene expression.

We have also moved genomic imprinting as a child of this term.

ValWood commented 6 months ago

'epigenetic programming of gene expression' GO:0043045 sounds as though it could also be used by yeast... it's also very similar to 'epigenetic regulation of gene expression'

In this respect the "post-fertilization" part of the label made the desired context very much clearer. so I pefer the previous label from a curation perspective.

Is there another way to make this clearer ? (of course it can have a taxon restriction), but the label does not seem to be precise enough.

pgaudet commented 6 months ago

Will add TC on GO:0043045 ~post-fertilization epigenetic regulation of gene expression~epigenetic programming of gene expression Never in NCBITaxon:Union_0000023 Fungi or Bacteria or Archaea

ValWood commented 6 months ago

right, I misunderstood.

I thought GO:0043045 post-fertilization epigenetic regulation of gene expression was the term you were relabelling. ignore.

pgaudet commented 6 months ago

No, you're right !! Correct label for GO:0043045 is epigenetic programming of gene expression

pgaudet commented 6 months ago

'epigenetic programming of gene expression' GO:0043045 sounds as though it could also be used by yeast... it's also very similar to 'epigenetic regulation of gene expression'

The distinction is the 'programming' part, ie there are some changes being made to the DNA that occur in early development and that persist in the organism, and that has the potential for regulating gene expression. Maybe some 'developmental' aspect is missing from the label, but it is in the definition.

Suggestions for improvement as welcome!

Pascale

ValWood commented 6 months ago

Maybe yeast people don't use the term"programming", it will be fine since it s taxon restricted, and its clear from the definition.