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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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sperm are not always ciliated #587

Closed ukemi closed 4 years ago

ukemi commented 4 years ago

To make a logical definition for sperm motility in GO, we need to be able to include sperm from organisms such as C. elegans. However, CL has this: male gamete and (capable of some flagellated sperm motility) and (capable of some sperm capacitation) and it is a subclass of ciliated cell (CL:0000064). I'm also not certain that worm sperm undergo capacitation.

See PMID:29879100

krchristie commented 4 years ago

Sperm are not even always motile. This paper discusses the non-motile sperm of seed plants. So, it seems to me that there are at least three types of sperm cells: -- sperm cell --- amoeboid sperm cell --- flagellated sperm cell --- non-motile sperm cell

Hackenberg & Twell. 2019. The evolution and patterning of male gametophyte development. Curr Top Dev Biol. 2019;131:257-298. doi:10.1016/bs.ctdb.2018.10.008. Dec 14. PMID:30612620

The reproductive adaptations of land plants have played a key role in their terrestrial colonization and radiation. This encompasses mechanisms used for the production, dispersal and union of gametes to support sexual reproduction. The production of small motile male gametes and larger immotile female gametes (oogamy) in specialized multicellular gametangia evolved in the charophyte algae, the closest extant relatives of land plants. Reliance on water and motile male gametes for sexual reproduction was retained by bryophytes and basal vascular plants, but was overcome in seed plants by the dispersal of pollen and the guided delivery of non-motile sperm to the female gametes. Here we discuss the evolutionary history of male gametogenesis in streptophytes (green plants) and the underlying developmental biology, including recent advances in bryophyte and angiosperm models. We conclude with a perspective on research trends that promise to deliver a deeper understanding of the evolutionary and developmental mechanisms of male gametogenesis in plants.

cmungall commented 4 years ago

Thank you for identifying this issue in CL

It's actually worse as CL asserts it's an animal cell:

image

While the focus of CL is metazoa, there is a need for an ontology to hold general groupings that span wider groups.

Also CL should strive to use language that does not cause confusion. Calling something "sperm" that is more specific than the label suggests is an anti-pattern. (note that we can always have taxon-specific synonyms for a more mammalian centric subclass if we like)

I propose

  1. that we remove the linkage between GLC and animal cell (and review what is currently under animal cell). In fact I question the utility of animal cell and eukaryotic cell. These predate TCs.
  2. we remove the logical definition from CL sperm cell (this is a bad definition in any case by the criteria I laid down in https://douroucouli.wordpress.com/2019/07/29/ontotip-dont-over-specify-owl-definitions/ and https://douroucouli.wordpress.com/2019/07/08/ontotip-write-simple-concise-clear-operational-textual-definitions/). We could make them taxon GCIs but I question the utility
  3. We add subclasses provided by Karen

Can @obophenotype/cell-ontology editors indicate agreement/disagreement

dosumis commented 4 years ago

So how do cilia and nematode sperm fit in to this picture?

ukemi commented 4 years ago

Nematode sperm do not have a flagellum. They are ameboid. There is also an issue here if we want to include plants. If I recall correctly from my days as a developmental biologist, plants do not segregate their germ line (see the graph above). Comments from @tberardini or @vanaukenk might be helpful here.

dosumis commented 4 years ago

Does movement by pseudopod count as ameboid? In which case C.elegans sperm classified as ameboid sperm (from PMID:29879100). Peraps worth ading motile and non-motile sibling classes.

ukemi commented 4 years ago

See this paper PMID:19295707

krchristie commented 4 years ago

Peraps worth ading motile and non-motile sibling classes.

I think that's a good idea. It seems to me that in order to make an equivalence axiom for the GO term 'sperm cell motility', it would be better to use a CL term 'motile sperm cell' rather than just 'sperm cell' since the latter isn't necessarily motile. So that would modify my earlier suggestion to this:

-- sperm cell --- motile sperm cell ---- amoeboid sperm cell ---- flagellated sperm cell --- non-motile sperm cell

nicolevasilevsky commented 4 years ago

is there action needed on this ticket?

ukemi commented 4 years ago

We need a release so we can import the new terms.

nicolevasilevsky commented 4 years ago

I think this can be closed, please reopen if needed.