Does OMP need separate terms for population growth, cell population growth, and vegetative cell population growth?

[dsiegele]

Katie, an undergrad in my lab, has been annotating papers that describe altered growth phenotypes, which led me to start working on this branch of the ontology again.

Currently, OMP has phenotype terms for population growth, cell population growth (is_a population growth), and also vegetative cell population growth (is_a cell population growth). I made the cell population growth and vegetative cell population growth terms because they are present in FYPO. However, I've started to think i) that some of the terms are redundant and ii) this level of granularity creates confusion (at least for me :-) ) about what terms to use and I don't think that OMP needs this level of granularity.

I started by looking at related terms in other ontologies. I've copied the terms and definitions at the bottom of this post.

i) Aren't cell population growth and vegetative cell population growth redundant? It think it makes biological sense for some phenotypes, such as morphology, to distinguish between vegetative cells and other types of cells, but not for growth.

I propose that we make the vegetative cell population growth phenotype terms obsolete and add them as synonyms of a higher level term.

ii) I am not sure if it is useful for OMP to distinguish between growth of a population and growth of a cell population. In GO, the only term I could find related to cell population growth is "cell population proliferation," which is supposed to be used for proliferation of a cells within a multicellular organism.

In FYPO "cell population growth" is a child of FYPO:000003 cell population phenotype: A phenotype that is observed at the level of a population of cells. In OMP, would it be useful to have separate terms for populations of single-celled microorganisms and population of multi-cellular microorganisms? Instead, we could make a distinction between populations of cellular microbes and populations of viruses. Maybe instead of cell population growth have cellular population growth.

Population terms in other ontologies
population OBI:0000181
http://purl.obolibrary.org/obo/OBI_0000181
A population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area.

cell population proliferation GO_0008283 is_a GO:0008150 biological process
http://purl.obolibrary.org/obo/GO_0008283
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
comment
_This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.

single-celled organism vegetative growth phase GO:0072690 is_a GO:0044848 biological phase is_a GO:0008150 biological process
http://purl.obolibrary.org/obo/GO_0072690
A phase of population growth during which single celled organisms reproduce by budding, fission, or other asexual methods.

reproduction of a single-celled organism GO:0032505 is_a GO:0000003 reproduction is_a GO:0008150 biological process
http://purl.obolibrary.org/obo/GO_0032505
The biological process in which new individuals are produced by one or two single-celled organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.

reproductive process in single-celled organism GO:0022413 is part_of GO:0032505
http://purl.obolibrary.org/obo/GO_0022413
A process, occurring at the cellular level, that is involved in the reproductive function of a single-celled organism.

cell population phenotype FYPO:0000003
http://purl.obolibrary.org/obo/FYPO_0000003
A phenotype that is observed at the level of a population of cells.

cell population growth phenotype FYPO:0000139 is_a FYPO:0000003 cell population phenotype
http://purl.obolibrary.org/obo/FYPO_0000139
A cell phenotype that affects the rate or extent of cell population growth.

vegetative cell population growth phenotype FYPO_0001358
http://purl.obolibrary.org/obo/FYPO_0001358
A cell phenotype that affects the rate or extent of cell population growth in the vegetative growth phase of the life cycle.

[jimhu-tamu]

Decisions - is this the consensus?

• population growth and vegetative growth are equivalent and term merges or obsoletions should be done.
• cellular vs acellular (?), e.g. viruses
  • cellular not cell, which is inclusive of microbes that are not single cells such as filaments.

[jimhu-tamu]

for later: fruiting bodies. slugs etc.

[dianeoinglis]

cell population growth and veg cell population growth may overlap but population growth can occur in non-veg cells such as those undergoing meiosis during spore production.

Also, keep in mind that fungi are considered both unicellular and sometimes a multicellular orgamism such as during hyphal or pseudohyphal growth (where cells remain attached), during growth as a mycelium or during sporulation.

That said, I agree with the proposal to obsolete the veg terms.

Diane