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Pathogen-Host Interaction Phenotype Ontology
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Re-structure population growth terms #290

Closed CuzickA closed 3 years ago

CuzickA commented 3 years ago

see #288

This branch should only contain terms for unicellular organisms eg yeast, bacteria.

Term label edits (and update defs) 5a4dbcc PHIPO:0000162 population growth phenotype -> unicellular population growth phenotype PHIPO:0000414 abnormal population growth-> abnormal unicellular population growth PHIPO:0000405 normal population growth->normal unicellular population growth

@jseager7 please could you pull out the sessions these terms have been used in as I will probably have to re-annotate some. Thanks.

CuzickA commented 3 years ago

Plan image

1) Move increased resistance to chemical increased sensitivity to chemical out of 'abnormal population growth' and place under 'single species phenotype' This will require a new grouping term NTR: Response to chemical phenotype and edit to terms def to indicate that it can be for 'an individual or a population' also NTR: normal growth on chemical (@ValWood should we have a term specify each chemical here, or add to condition?) a new ticket will be created for this #291

2)Move resistance to stress sensitive to stress out of 'abnormal population growth' and place under 'single species phenotype' This will require a new grouping term NTR: Response to stress and edit to terms def to indicate that it can be for 'an individual or a population' also NTR: normal growth on stress agent (@ValWood should we have a term specify each stress agent here?) a new ticket will be created for this #292

3) Move auxotrophy phenotype out of 'abnormal population growth' and place under 'single species phenotype' This will require new grouping terms NTR: Response to nutrient, auxotrophic growth, prototrophic growth (create terms with nutrient in term label) and edit to terms def to indicate that it can be for 'an individual or a population' a new ticket will be created for this #293

ValWood commented 3 years ago

For stress we will include things like the class of stress (DNA damage, oxidative, osmotic), but include the actual chemical MMS, H202, MgCl, CaCl ....

jseager7 commented 3 years ago

please could you pull out the sessions these terms have been used in as I will probably have to re-annotate some. Thanks.

@CuzickA There are no annotations with PHIPO:0000162 or PHIPO:0000414.

The only annotations with PHIPO:0000405 'normal population growth' are for the following publications:

(current as of 30 November)

CuzickA commented 3 years ago

image

In addition to top comment I will also need to make the below terms 'unicellular' PHIPO:0000974 decreased population growth PHIPO:0001124 decreased population growth on erucic acid carbon source PHIPO:0001127 decreased population growth on myristic acid carbon source PHIPO:0001125 decreased population growth on oleic acid carbon source PHIPO:0001126 decreased population growth on palmitic acid carbon source PHIPO:0001085 decreased population growth rate PHIPO:0000975 increased population growth PHIPO:0001084 increased population growth rate

@jseager7 please could you pull out the sessions where these terms have been used, thanks. @ValWood From memory I think the carbon source terms have been annotated to filamentous pathogen (Fg). maybe they need to be moved out of decreased population growth and added as another group under single species parentage??

ValWood commented 3 years ago

Can't you just move them to the new terms that do not specify population or individual?

CuzickA commented 3 years ago

Yes, that was what I was thinking. They will need a new grouping term maybe Response to carbon source phenotype?

ValWood commented 3 years ago

I think these can just go under the "response to nutrient" grouping term?

CuzickA commented 3 years ago

I think these can just go under the "response to nutrient" grouping term?

Yes, I agree thanks.

jseager7 commented 3 years ago

@CuzickA Here's the sessions for the above terms (current as of 30 November)

CuzickA commented 3 years ago

Thanks @jseager7

CuzickA commented 3 years ago

Edit term labels and defs 68e5525 f237e98

PHIPO:0000974 decreased population growth-> decreased unicellular population growth PHIPO:0001085 decreased population growth rate -> decreased unicellular population growth rate PHIPO:0000975 increased population growth-> increased unicellular population growth PHIPO:0001084 increased population growth rate -> increased unicellular population growth rate

image

Note the 4 carbon source terms will be moved soon

CuzickA commented 3 years ago

image

I have moved some terms out of population growth, now looks like this.

Next: think about the 'dimorphic terms'

CuzickA commented 3 years ago

image

After todays meeting we decided upon the following changes as the new unicellular growth and hyphal growth phenotypes should cover the requirements of dimorphic pathogens

PHIPO:0000163 abnormal population growth during dimorphic yeast-form Merge into PHIPO:0000414 abnormal unicellular population growth DONE 492b1d2

PHIPO:0000123 normal population growth during dimorphic yeast-form merge into PHIPO:0000405 normal unicellular population growth DONE 4d78315

PHIPO:0000963 normal population growth during dimorphic hyphal-form merge into PHIPO:0001210 normal hyphal growth DONE cca865a

Obsolete ‘PHIPO:0000177 yeast-form growth phenotype’ DONE e99a1d2

Now looks like this image

jseager7 commented 3 years ago

These new terms look like they'll be a lot easier to map to uPheno patterns.

@ValWood does the Gene Ontology have any process terms for 'unicellular population growth' or simply 'population growth'? I can't find any exact matches in GO. The terms that do make reference to unicellular organism populations are concerned with the regulation of a process in the population, such as 'regulation of filamentous growth of a population of unicellular organisms' (GO:1900428).

It would make pattern mapping easier if there were terms just describing the growth process of a population of unicellular organisms. Has GO already decided against creating population-level versions of process terms, for the sake of preventing an explosion of new terms?

CuzickA commented 3 years ago

Edit defs for below

unicellular population growth phenotype old def A single species population phenotype that affects the rate or extent of the increase in the number of unicellular organisms in the population (i.e organismal growth and reproduction). new def A single species population growth phenotype that affects the rate or extent of the increase in the number of unicellular organisms in the population (i.e organismal growth and reproduction).

abnormal unicellular population growth old def A single species population phenotype in which a population of unicellular organisms grow abnormally. new def A single species population growth phenotype where the rate or extent of the increase in the number of unicellular organisms in the population (i.e organismal growth and reproduction) is lesser or greater than normal.

decreased unicellular population growth old def A single species phenotype in which the growth of a population of unicellular organisms is decreased relative to normal. Decreased growth may reflect a reduced growth rate (i.e. slower growth), growth that occurs to a lesser extent than normal, or both. new def A single species population growth phenotype where the rate or extent of the increase in the number of unicellular organisms in the population (i.e organismal growth and reproduction) is lesser than normal.

decreased unicellular population growth rate old def A single species phenotype in which the growth of a population of unicellular organisms is slower than normal. new def A single species population growth phenotype where the rate of the increase in the number of unicellular organisms in the population (i.e organismal growth and reproduction) is slower than normal.

increased unicellular population growth old def A single species phenotype in which the growth of a population of unicellular organisms is increased relative to normal. Increased growth may reflect an increased growth rate (i.e. faster growth), growth that occurs to a greater extent than normal, or both. new def A single species population growth phenotype where the rate or extent of the increase in the number of unicellular organisms in the population (i.e organismal growth and reproduction) is greater than normal.

increased unicellular population growth rate old def A single species phenotype in which the growth of a population of unicellular organisms is faster than normal. new def A single species population growth phenotype where the rate of the increase in the number of unicellular organisms in the population (i.e organismal growth and reproduction) is faster than normal.

normal unicellular population growth old def A single species population phenotype in which a population of unicellular organisms grow normally (i.e. indistinguishably from wild type). new def A single species population growth phenotype where the rate or extent of the increase in the number of unicellular organisms in the population (i.e organismal growth and reproduction) is normal (i.e. indistinguishable from wild type).

Above all DONE ef53554

CuzickA commented 3 years ago

Next: reannotate sessions listed above

ValWood commented 3 years ago

Re:

These new terms look like they'll be a lot easier to map to uPheno patterns.

It would make pattern mapping easier if there were terms just describing the growth process of a population of unicellular organisms. Has GO already decided against creating population-level versions of process terms, for the sake of preventing an explosion of new terms?

I don't think it will be easy (or even possible to logically define the population growth terms. I'm not sure that these have logical defs in FYPO (mah11?) These term are a bit of an outlier. GO does not represent these terms because they aren't concerned with population level observations. These are out of scope for GO.

Really, they are just about viability (whether the population survives of not), rather than a specific process.

such as 'regulation of filamentous growth of a population of unicellular organisms' (GO:1900428).

I'm not even sure that these belong in GO either so they will probably disappear.

mah11 commented 3 years ago

I'm not sure that these have logical defs in FYPO

Actually a lot of them do, but it's an inelegant hack that probably won't help for PHIPO. The terms for vegetative population growth have logical definitions using GO:0072690 ("single-celled organism vegetative growth phase"); it's a hack because the GO term descirbes a life cycle stage and is in the "biological phase" branch.

FYPO terms for population growth in other life cycle stages (not many) don't have LDs.

CuzickA commented 3 years ago

Terms updated for above sessions. closing ticket.