OTR: Align GO and Reactome on ciliary processes

[paolaroncaglia]

@JohnvanDam @krchristie @deustp01

As part of the cilia GO project, we need to make sure that GO and Reactome align on representation of ciliary processes. Reactome recently worked on this area, this is the overall pathway we should look at:

Assembly of the primary cilium (R-HSA-5617833) [Homo sapiens] http://www.reactome.org/content/detail/R-HSA-5617833 http://www.reactome.org/PathwayBrowser/#/R-HSA-5617833&PATH=R-HSA-1852241

Issues we need to address first:

The Reactome pathway refers explicitly to the primary cilium in its name. The summation quotes, more specifically, the non-motile primary cilium. We need to tie this alignment work with our planned re-naming of cilia types, see https://github.com/geneontology/go-ontology/issues/12462 Which of these 4 suggested classes does the Reactome pathway cover?

1) 9+0 non-motile cilia (which include authentic primary cilia, but are not limited to them), 2) 9+0 motile cilia (which include classic nodal cilia, but are not limited to them), 3) 9+2 non-motile cilia, 4) 9+2 motile cilia (which include so-called flagella and conventional motile cilia).

Karen Rothfels at Reactome authored the entry on ‘Assembly of the primary cilium’, so we may wish to consult with her here. In the meantime, Peter, please let us know if you have any comments, thanks.

GO currently has terms for

motile cilium primary cilium

• motile primary cilium
• nonmotile primary cilium

and for

cilium assembly

• motile cilium assembly
• motile primary cilium assembly
• nonmotile primary cilium assembly

We may need to merge some terms (both CC and BP) and we need to make sure what can correctly merge into what/correctly rehouse annotations if necessary. Number of direct, manual experimental annotations to BP terms:

cilium assembly [499 for 355 proteins]

• motile cilium assembly [37 for 34 proteins]
• motile primary cilium assembly [5 for 5 proteins]
• nonmotile primary cilium assembly [150 for 96 proteins]

Thanks, Paola

[paolaroncaglia]

Thanks @krchristie .

[paolaroncaglia]

Reopening because Peter Satir replied:

“My suggestion is to look at the classification of living organisms which is Appendix 2 in my version of Campbell’s Biology, then Google the phylum and “cilia”. In plants, there are no cilia in Angiosperms and conifers –but in a slightly different phylum - Gingko (a common city tree) has motile ciliated sperm as do mosses, bryophytes etc. Among the protists and fungi there are probably other phyla where cilia are absent (slime molds, for example) but I am familiar only with the typical examples (e.g. Dictyostelium, Physarum). I think all animal phyla have either motile or sensory cilia or both.”

Currently, ‘cilium’ and ‘cilium assembly’ are restricted to relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota

To keep this simple, I’d stick to

• [x] “In plants, there are no cilia in Angiosperms and conifers” This should mean adding the same never_in taxon rules to ‘cilium’ and ‘cilium assembly’ as in https://github.com/geneontology/go-ontology/issues/12672#issuecomment-251089425, where Tanya advised:

never in Magnoliophyta (NCBITaxon:3398) never in Zygnematales (NCBITaxon:3176) never in Gnetales (NCBITaxon:3378) never in Coniferophyta (NCBITaxon:3312)

“The evolution of land plant cilia http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04197.x/full (PMID:22691130) See Figure 3 and accompanying legend, "Land plant phylogeny and the loss of cilia. (a) Cladogram showing the relationship between Chlorophyte, Charophyte (vertical black bar) and land plant (vertical green bar) groups. In both the Charophytes and land plants, where produced, cilia are restricted to sperm cells. The most parsimonious explanation for the distribution of cilia in land plants is two loss events (red stars): once at the base of the Angiosperms and once in the Gymnosperms, where Ginkgo and the cycads diverge from the nonciliated conifers and Gnetales.””

• [x] “Among the protists and fungi there are probably other phyla where cilia are absent (slime molds, for example) but I am familiar only with the typical examples (e.g. Dictyostelium, Physarum).”

PMID: 16824949 says “Having arisen early in eukaryotic evolution, cilia can be found across a broad phylogenetic spectrum with certain exceptions including Cyanidioschyzon, Arabidopsis, Dictyostelium, and Saccharomyces (Cavalier-Smith, 2002). Although cilia are only found in select cell types in invertebrates, such as the dendritic ends of sensory neurons of Caenorhabditis or in the sperm and sensory neurons of Drosophila, they are present almost ubiquitously in vertebrate cells.” Cavalier-Smith, 2002 = PMID: 11931142

So I’ll add ‘cilium’ and ‘cilium assembly’ never_in Dictyostelium.