NTR: need terms for cell morphology phenotypes described in Campos et al.

[dsiegele]

Genome-wide phenotypic analysis of growth, cell morphogenesis and cell cycle events in Escherichia coli (2018) Manuel Campos, Sander K. Govers, Irnov Irnov, Genevieve S. Dobihal, François Cornet, and Christine Jacobs-Wagner

[dsiegele]

Created following terms:

OMP:0007916 ! decreased vegetative cell width def. "An altered cell size phenotype in which the width of a nonspherical cell in the vegetative growth phase of the life cycle is decreased relative to a designated control."

OMP:0007917 ! cell size variability within a cell population phenotype

OMP:0007922 ! absence of cell size variability within a cell population

OMP:0007921 ! presence of cell size variability within a cell population

OMP:0007918 ! altered variability in cell size within a cell population

OMP:0007923 ! decreased variability in cell size within a cell population

OMP:0007925 ! abolished variability in cell size within a cell population .....is_a child of OMP:0007922 ! absence of cell size variability within a cell population

OMP:0007924 ! increased variability in cell size within a cell population

Still need to write definitions.

[dsiegele]

The following terms were made. Still need to write definitions.

OMP:0007976 ! altered cell length variability OMP:0007979 ! increased cell length variability OMP:0007980 ! decreased cell length variability

OMP:0007977 | altered cell width 2019-07-28 changed to altered cell diameter These two terms already existed and need to be merged with diameter terms: OMP:0007665 | decreased cell width and OMP:0007664 | increased cell width

OMP:0007978 | altered cell width diameter variability 2020-11-29 changed to cell diameter OMP:0007981 | decreased cell width diameter variability OMP:0007982 | increased cell width diameter variability

OMP:0007993 | altered cell surface area OMP:0007994 | decreased cell surface area OMP:0007995 | increased cell surface area

OMP:0007996 | altered cell surface area variability OMP:0007997 | decreased cell surface area variability OMP:0007998 | increased cell surface area variability

OMP:0007999 | altered cell surface area-to-volume ratio OMP:0000009 | decreased cell surface area-to-volume ratio OMP:0000019 | increased cell surface area-to-volume ratio

OMP:0000025 | altered cell surface area-to-volume ratio variability OMP:0000032 | decreased cell surface area-to-volume ratio variability OMP:0000038 | increased cell surface area-to-volume ratio variability

OMP:0007989 | altered cell volume OMP:0007719 | decreased cell volume OMP:0007721 | increased cell volume

OMP:0007990 | altered cell volume variability OMP:0007991 | decreased cell volume variability OMP:0007992 | increased cell volume variability

OMP:0000193 | altered cell aspect ratio OMP:0000223 | decreased cell aspect ratio OMP:0000226 | increased cell aspect ratio

OMP:0000227 | altered cell aspect ratio variability OMP:0000233 | decreased cell aspect ratio variability OMP:0000235 | increased cell aspect ratio variability

OMP:0000044 | altered cell circularity OMP:0000051 | decreased cell circularity OMP:0000064 | increased cell circularity

OMP:0000138 | altered cell circularity variability OMP:0000170 | decreased cell circularity variability OMP:0000186 | increased cell circularity variability

OMP:0000251 | altered cell division ratio variability OMP:0000257 | decreased cell division ratio variability OMP:0000259 | increased cell division ratio variability

OMP:0000260 | altered nucleoid area OMP:0000261 | decreased nucleoid area OMP:0000262 | increased nucleoid area

OMP:0000263 | altered nucleoid area variability OMP:0000264 | decreased nucleoid area variability OMP:0000265 | increased nucleoid area variability

OMP:0000266 | altered cell population growth rate OMP:0000270 | decreased cell population growth rate OMP:0000271 | increased cell population growth rate

[dsiegele]

The following terms were made. Still need to write definitions

OMP:0000273 ! altered cell perimeter OMP:0000275 ! decreased cell perimeter OMP:0000276 ! increased cell perimeter

OMP:0000277 ! altered cell perimeter variability OMP:0000278 ! decreased cell perimeter variability OMP:0000279 ! increased cell perimeter variability

OMP:0000284 ! altered cell population growth yield OMP:0000285 ! decreased cell population growth yield OMP:0000286 ! increased cell population growth yield

OMP:0000287 ! altered fraction of non-constricted cells OMP:0000288 ! decreased fraction of non-constricted cells OMP:0000292 ! increased fraction of non-constricted cells

OMP:0000293 ! altered fraction of cells with one nucleoid OMP:0000297 ! decreased fraction of cells with one nucleoid OMP:0000298 ! increased fraction of cells with one nucleoid

OMP:0000300 ! altered fraction of cells with two nucleoids OMP:0000301 ! decreased fraction of cells with two nucleoids OMP:0000302 ! increased fraction of cells with two nucleoids

OMP:0000303 ! altered correlation between the degrees of constriction of the nucleoid and the cell OMP:0000305 ! decreased correlation between the degrees of constriction of the nucleoid and the cell OMP:0000313 ! increased correlation between the degrees of constriction of the nucleoid and the cell

OMP:0000314 ! altered degree of nucleoid constriction at the onset of cell constriction OMP:0000315 ! decreased degree of nucleoid constriction at the onset of cell constriction OMP:0000316 ! increased degree of nucleoid constriction at the onset of cell constriction

[dsiegele]

I'd like to discuss term names, definitions, and placement of the terms being made to annotate cell morphology and growth phenotypes described in the paper by Campos et al.

Note: I haven't finished writing this

1) For phenotypes such as motility, the independent phenotype terms 'presence of motility' and 'absence of motility' have an obvious biological meaning. For some other phenotypes, such as cell length or population growth rate, the terms created by our pattern seem less natural--see examples below. Should we continue to follow the pattern 'presence of' and 'absence of' or come up with an alternative?

Example 1: cell length If we follow the pattern used so far, the independent terms would be called presence of cell length and absence of cell length.

• presence of cell length def. A cell morphology phenotype used to describe the mean length of a microbial cell of the designated strain under the designated conditions.
• absence of cell length I'm not sure that it makes sense to create this term except for completeness. I am also afraid that having it would lead to confusing annotations.

Possible alternative names I've thought of:

• presence of some cell length
• presence of cell length in designated control; cell length baseline for designated control; cell length standard in designated control; reference cell length -- I rejected these because while they might be OK when comparing phenotypes for parent and mutant strains. I don't think they work so well for making independent annotations.

Example 2: population growth rate

• presence of population growth rate def. A population phenotype used to describe the growth rate (generations per h) of a microbial population of the designated strain under the designated conditions.
• absence of population growth rate def. A population phenotype where the growth rate of a microbial population is zero.

2) Width or diameter? We discussed this previously (issue #248) and decided to merge width and diameter terms. When reviewing the topic today, I noticed that the definitions for width and diameter are different: width is defined to be used for nonspherical cells and diameter is defined to be used for spherical cells. Does this mean we cannot merge them? If they cannot be merged, should we keep both and change names to make usage clear? Make width terms obsolete until someone wants to annotate the morphology for Walsby's square archaeon?

3) Placement of cell morphology terms in OMP.

• Cell morphology phenotype is currently located under microbial phenotype/cell phenotype/cellular physical quality phenotype/. However, authors typically measure some number of cells and then report the result as mean cell length, mean cell diameter, etc. Does this mean that cell morphology should be a cell population phenotype instead or in addition to?

• Variability in cell morphology terms were made subclasses of cell population phenotype. Should they also link somehow to the cell phenotype terms.

[dsiegele]

Hi Michelle,

The terms made in September 2018 are in OLS, but the ones I made 10 days ago were made after the July release. The new ones should show up when Suvvi does the release in August.

Debby

OMP:0007917 cell size variability within a cell population phenotype OMP:0007922 absence of cell size variability within a cell population OMP:0007918 altered variability in cell size within a cell population OMP:0007923 decreased variability in cell size within a cell population OMP:0007925 abolished variability in cell size within a cell population OMP:0007924 increased variability in cell size within a cell population

On Sun, Aug 2, 2020 at 4:30 PM Michelle notifications@github.com wrote:

Hi Debby, I was looking to see the new terms from this issue (the ones before a couple weeks ago) but I don't see them on the wiki or in OLS. Have they been committed to OMP? Michelle

@nsuvarnaiari https://github.com/nsuvarnaiari

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[mgiglio99]

Hi,

Thanks Debby - I found them just after I sent the comment (of course) - I deleted the comment but github had already sent the email.

Some thoughts ahead of the call tomorrow.

For 1. I don't think we have to make independent phenotypes for every node. As you say, for some phenotypes they just don't make sense. I think we already have terms without those - for example "cell morphology phenotype" does not have "presence of..." and "absence of..." children.

For 2. I guess width could also apply to rod shaped cells too - although I was just looking up terminology and apparently for cylinders (approximation of a rod shaped cell) this is called diameter, not width. So, we could make diameter apply to rods, spheres or anything with a circular cross section (this would also include the spirals). Or we could keep diameter for just spheres and use width for anything else. I think it would be fine either way, we just have to decide what we think will be most intuitive to the community and define everything clearly.

For 3. a. I think that the assay (looking at 100 cells vs one cell) is separate from the phenotype. However the experiment is done, once they conclude that there is a phenotype, that is the key thing - so I don't think we need to link it to population. b. Yes, I think the variability terms should also link to cell phenotype

Looking forward to chatting tomorrow. : ) Michelle

@nsuvarnaiari

[mgiglio99]

Conclusions from discussion 8/3

1. We will have some nodes with presence/absence children and some without, based on where it makes biological sense. The guideline will be that if there are presence/absence children in a node, then one of those should be be used to annotate the control. If there isn't then the parent of that node should be used to annotate the control. Debby will start working through the nodes in OMP to check for the need for presence/absence terms.

2. We decided to use "diameter" as the term for any cell that has s circular cross section. (We will worry about the cube-shaped cells in the future if it ever comes up.) Therefore, we will merge the existing width terms into the diameter terms and expand the definition of the diameter terms to include not just spheres but any cell with a circular cross section.

3.a. General consensus is that terms like 'cell length' and 'cell diameter' do not need to be applied at a population level. They can be considered phenotypes of a single cell (even if you need to look at many cells to determine what the phenotype is.) 3.b. Since the variability terms are describing something that is a comparison of a population of cells to each other and a measure of how similar or not they are to each other, then they must be at the population level - but they should also link into the cell phenotype node as well.

[dsiegele]

Finished making the terms needed to annotate the cell morphology and cell cycle phenotypes in Campos et al. (2018). Note that some of the terms described above were changed.

Still need to finish writing definitions. Need to check that variability phenotypes connect to the cell phenotype node, as well as the cell population node.