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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Should prokaryote cells be in CL #722

Open cmungall opened 4 years ago

cmungall commented 4 years ago

Do prokaryotes have cell types?

Currently only 3 classes

heterocysts are cool.. from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845205/

Many cyanobacterial species are capable of nitrogen fixation. However, oxygenic photosynthesis and nitrogen fixation are incompatible processes because nitrogenase is inactivated by oxygen. Cyanobacteria mainly use two mechanisms to separate these activities: a biological circadian clock to separate them temporally, and multicellularity and cellular differentiation to separate them spatially. For example, the unicellular Cyanothece sp. strain ATCC 51142 stores glycogen during the day and fixes nitrogen at night (Toepel et al. 2008), whereas the filamentous Trichodesmium erythraeum IMS101 fixes nitrogen during the day in groups of specialized cells (Sandh et al. 2009). Heterocyst-forming cyanobacteria differentiate highly specialized cells to provide fixed nitrogen to the vegetative cells in a filament.

However, if we are going to house prok cells in CL we need to do a better job or at least mark that as hugely incomplete. Even within cyanobacteria there are other cell types than heterocysts, e.g. spore-like akinetes, and the cells of motile hormogonia filaments.

I suggest for now we come up with a standard AP (@matentzn ?) to declare this branch highly incomplete and remain open to moving this out into a more dedicated ontology once resources are available.

I added a TC (#707)

lubianat commented 4 years ago

Would types such as "coccus" and "bacillus" (and so on) count as prokaryotic cell types?