paolaroncaglia
commented
7 years ago Also for future work, much related to ciliary processes but also extending to some non-ciliary ones:
- [ ] revise children of GO:0048870 'cell motility':
From an old email from Chris to the ontology group:
“I think it's worth looking at the mix of asserted children here and trying to approach this differently
is_a GO:0044763 ! single-organism cellular process is_a GO:0006928 ! cellular component movement is_a GO:0048870 ! cell motility is_a GO:0001539 ! cilium or flagellum-dependent cell motility is_a GO:0003411 ! cell motility involved in camera-type eye morphogenesis is_a GO:0016477 ! cell migration is_a GO:0021805 ! cell movement involved in somal translocation is_a GO:0021814 ! cell motility involved in cerebral cortex radial glia guided migration is_a GO:0030317 ! sperm motility is_a GO:0043107 ! type IV pilus-dependent motility is_a GO:0070358 ! actin polymerization-dependent cell motility is_a GO:0071975 ! cell swimming is_a GO:0071976 ! cell gliding is_a GO:0090247 ! cell motility involved in somitogenic axis elongation is_a GO:0097230 ! cell motility in response to potassium ion is_a GO:0097231 ! cell motility in response to calcium ion
What are the different mechanisms of motility? Are they disjoint? Can something be 'cell swimming' and cilium-directed and migration at the same time?
It looks like the differentia are a mix of mechanism (e.g. cilium, pilus), context (involved in, response to) or a descriptive measure of the motion or immediate environment (swimming, gliding). Or migration which seems insufficiently differentiated.
On closer examination of the children, the last category seems to disappear and that these are actually cryptic mechanism descriptions too: gliding is achieved through secretion of adhesion molecules and 'swimming' is either the cytoskeleton contracting the cell or GO:0071977 which seems insufficiently differentiated from its parent
I'd prefer to ground things more mechanistically or contextually.
Once this is done it gives us a better way to answer questions about where 'sperm motility' can go. Are there any other possible mechanisms other than cilium? If not, then a hidden GCI is justified. Does this hold for any cell with an X as part, where X is a possible mechanism of motility?”
ValWood
krchristie
This ticket is a placeholder for potential future work on cilia-related terms, if we ever get the chance/funding/collaborations to do so:
[ ] We may want to look at other children of ‘cilium organization’, namely ‘cilium disassembly’ and (not existing yet) ‘cilium maintenance’.
[ ] Add term for ‘(de novo?) centriole assembly involved in ciliated olfactory receptor neuron differentiation’ (with related synonyms ‘multiciliation’ and ‘multiciliogenesis’) if/when new research clarifies this point (from PMID:25047614): “There are other situations in which multiple centrioles form, and the relationship between these and the deuterosome pathway is not clear. One example is the olfactory sensory neurons, which are the main sensory cells in the olfactory epithelium. In these neurons, dendrites extend towards the nasal cavity, ending in a knob containing 10–30 centrioles from which cilia project to the epithelial surface. Ultrastructural studies suggested that these centrioles assemble near-simultaneously in the cell body and migrate to the dendritic knob, but whether the centrioles are nucleated from pre-existing centrioles or deuterosome-like structures is not known.” Will need adding via TG beforehand ‘ciliated olfactory receptor neuron differentiation’, pointing to CL:0000847 (make sure the GO term has synonyms for ciliated olfactory sensory neuron, ciliated sensory neuron).
[ ] Add term for ‘de novo centriole assembly involved in asexual reproduction’ (or a more specific one? without any cilia-related synonyms) to describe this (from PMID:25047614): “Centriole number control also differs from that of somatic cycling cells in embryos in which the centrioles are not derived from the sperm. In most animals, the sperm cell has one or two centrioles that are introduced into the egg upon fertilization, then duplicated, initiating the pathway described above for cycling cells. However, in some organisms, the embryo develops parthenogenetically, without sperm, thus centrioles must be formed de novo, and number control exerted after formation. For example, in insects of the hymenoptera order, hundreds of centrioles form de novo during the late stages of oogenesis. These centrioles then recruit pericentriolar material and form microtubule asters. From these many centrosomes, only two become associated with the female pronucleus and form the mitotic spindle, whereas others degenerate, thus establishing the correct ratio of centrioles to nuclei.”. Maybe check with FlyBase about taxon constraints.
[ ] Polarisation of cilia, do we need it and where should it be placed? (See PMID:25291643)
[ ] How can we represent tissue level polarisation of MCCs? (See PMID:25291643) Use existing ‘establishment of tissue polarity’ (or its child ‘establishment of planar polarity’)? Karen Christie noted previously: “One possibly useful comment I have is that my understanding of tissue level polarization via the planar cell polarity (PCP) pathway is that the PCP pathway is often upstream and critical to the development of the orientation of cilia in singly ciliated cells, e.g. in the hair cells of the ear that form kinocilia and arrays of stereocilia. I can't recall coming across anything specific about any role of the PCP pathway in the development of MCC's (though this may be due to failure of my memory). However, it wouldn't surprise me if the PCP pathway is equally important in MCC's as in singly ciliated cells.”
[ ] Address Peter Satir's concern that "in some organisms the multiple cilia form a distinct organelle (mussel gill laterofrontal cilia, ctenphore comb plates) and this isn’t captured at all.".
[ ] It would be great if more players could be annotated to multiciliation-related terms. A good starting point to find papers could be the review PMID:25291643 from 2014. Plus these 2 reviews that Karen pointed out previously: 1) Meunier A, Azimzadeh J. Multiciliated Cells in Animals. Cold Spring Harb Perspect Biol. 2016 Aug 31. pii: a028233. doi: 10.1101/cshperspect.a028233. [Epub ahead of print] PubMed PMID: 27580630. 2) Ohata S, Alvarez-Buylla A. Planar Organization of Multiciliated Ependymal (E1) Cells in the Brain Ventricular Epithelium. Trends Neurosci. 2016 Aug;39(8):543-51. doi: 10.1016/j.tins.2016.05.004. Epub 2016 Jun 13. Review. PubMed PMID: 27311928.
[ ] Indeed, ideally, all PMIDs used as dbxrefs for GOC:cilia terms should be annotated, if they're not already, if they’re not review papers and if they contain info appropriate for gene product curation…