obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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not all organisms existence begins with a zygote stage #1509

Open srobb1 opened 5 years ago

srobb1 commented 5 years ago

'anatomical structure' has this axiom 'existence starts during or after some zygote stage'. This axiom is untrue for the asexual planarian that lacks any ability to sexually reproduce, and therefore, "A stage at which the organism is a single cell produced by means of sexual reproduction", never occurs. This organism reproduces solely through fission. There are many other cases of this axiom not being true for vertebrates and other invertebrates.

This article, Evolutionary perspectives on clonal reproduction in vertebrate animals, addresses many of the instances for which this axiom would be untrue for vertebrates.

Abstract "A synopsis is provided of different expressions of whole-animal vertebrate clonality (asexual organismal-level reproduction), both in the laboratory and in nature. For vertebrate taxa, such clonal phenomena include the following: human-mediated cloning via artificial nuclear transfer; intergenerational clonality in nature via parthenogenesis and gynogenesis; intergenerational hemiclonality via hybridogenesis and kleptogenesis; intragenerational clonality via polyembryony; and what in effect qualifies as clonal replication via self-fertilization and intense inbreeding by simultaneous hermaphrodites. Each of these clonal or quasi-clonal mechanisms is described, and its evolutionary genetic ramifications are addressed. By affording an atypical vantage on standard vertebrate reproduction, clonality offers fresh perspectives on the evolutionary and ecological significance of recombination-derived genetic variety."

Here are some invertebrate examples:

If we are talking specifically about fissiparity this would include a bunch of annelid worms, both polychaetes (marine bristleworms) and oligochaetes(earthworms)... other turbellarians other than just planaria as well as everyone's radially symmetric favorite: sea stars.

There are also invertebrates that reproduce clonally bypassing embryogenesis by their own power by budding too : Cniderians (Hydra), Porifera (Corals), some marine acoels like Convolutriloba.

I think the best solution would be to remove this axiom from 'anatomical structure'. This would alleviate the untrue issue as well as all of the descendant terms inheriting this axiom.

Thank you, Sofia

cmungall commented 5 years ago

For parthenogenic organisms: we can make a superclass of zygote stage, 'single cell stage', and use that.

Would it make sense to say:

('anatomical structure' and part-of some vertebrata) SubClassOf starts-during-or-after some 'single-celled stage'

Are there vertebrates that are exceptions?

We will also need to qualify preceded_by:

image

srobb1 commented 5 years ago

@cmungall

I think a vertebrate biologist would be better to chime in on if the single cell superclass would work. But from my understanding it seems good to me.

Does thepart-of some vertebrata in ('anatomical structure' and part-of some vertebrata) SubClassOf starts-during-or-after some 'single-celled stage' indicate that this is only for vertebrates? And does that mean that it does not apply for invertebrates and then this will work for planarians and the other invertebrates that don't have a zygote stage? If so, then I think it is perfect!

Sofia